CALABAR, Nigeria — The Nigerian army has been accused of massacring a large number of Shia Muslims in the town of Zaria in Nigeria’s northwestern Kaduna state over the course of three days this month. Shia sources say hundreds, perhaps as many as 1,000, have been killed in fighting, but those numbers could not be confirmed independently.

The Nigerian authorities claim that members of the radical Islamic Movement of Nigeria (IMN) had attempted to assassinate the Nigerian Army Chief of Staff, Lt. Gen. Tukur Buratai, on Dec. 12 when his motorcade was passing through a Shia procession.

The incident suggests just how fractured and extensive unrest can be in Nigeria’s deep interior, far from Lagos, the thriving commercial hub of Africa’s biggest economy.

The clashes in this case were not between security forces and the infamous terrorist forces of Boko Haram, a radical Sunni Muslim group now affiliated with the so-called Islamic State. This group is led by converts to Shia Islam originally inspired by the Iranian Revolution in 1979.

The Nigerian military police claimed in a report that some members of the IMN were crawling through grass towards Buratai’s car, aiming “to attack the vehicle with [a] petrol bomb,” while others “resorted to firing gunshots from the direction of the mosque.”

One witness told The Daily Beast that the Shia protesters placed burning tires on the road as a barricade to prevent the approaching Buratai and his entourage from passing, and then stoned his convoy, a claim that has been denied by the IMN.

Maj. Gen. Adeniyi Oyebade, commander of the army division in the area, said last week that the military acted because they had good intelligence that members of the Shia sect were gathering for an attack.

“I take that very seriously that the life of the [the chief of army staff] is under threat, and within the rules of engagement permissible by law, I had to bring the forces available to me to bring the situation under control and that was exactly what I did,” he said.

The IMN suffered many casualties, Oyebade said, but he insisted “there were also casualties among the security forces.”

The leader of the IMN, Ibrahim Zakzaky, was wounded in the fighting—and his son reportedly was killed. The Nigerian Army said it arrested both Zakzaky and his wife, Malam Zeenat Ibrahim.

Not surprisingly, Iranian officials were the first outside Nigeria to react. The country’s foreign ministry called the violence “unacceptable,” the official IRNA news agency reported, and officials summoned the Nigerian chargé d’affaires in Tehran to protest against the deadly clashes. Iranian President Hassan Rouhani also called his Nigerian counterpart, Muhammadu Buhari, to say that he expects the Nigerian government to compensate the families of the dead and injured.

Zakzaky, an Iranian-trained Shia theologian, became a proponent of Shia Islam around the time of the Iranian revolution in 1979, when he was inspired by the Ayatollah Khomeini. The overthrow of the Pahlavi dynasty by the Islamic Republic convinced Zakzaky that an Islamic revival was also possible in Nigeria. And on the sidelines, he may well have been encouraged by Iranian missionaries helping to establish and fund a Shia presence in Nigeria. In the last two decades, Iran has increased its influence here, and maintains a large diplomatic presence.

In 1996, when Nigerians faced repression under military rule, Zakzaky reportedly said, “Nigeria must become wholly Islamic and Allah proclaimed Lord of the entire nation.” That about half the population of Nigeria is Christian, and the vast majority of Muslims are Sunni, seems not to have deterred him.

Zakzaky is vehemently anti-American, and his supporters have been involved in many violent clashes with the state over the decades. Hundreds of his soldiers are in prison, and for approximately nine years during the 1980s and 1990s, Zakzaky was incarcerated by Nigeria’s military leaders, who accused him of civil disobedience.

The Shia leader has grown increasingly confident he can build a permanent Islamic state within the country. He denies his movement gets any funding from Tehran, but many of its leaders and adherents regularly visited Iran or have studied there.

Zakzaky has made good use of the media in reaching out to his followers. Film documentaries of religious leaders are translated into the local Hausa language, with hundreds of DVDs sold to locals every month, and two news magazines—Pointer Express, published in English, and Mizan, published in Hausa—have existed for years.

The IMN also operates an official English language website, with similar versions in the Hausa language and Arabic. Issues such as Shia perspectives of Sunni Islam, radicalism, terrorism, nationalism, and secularism, as well as the discourses of Khomeini and the current Supreme Leader, Ali Khamenei, are regularly presented on the website.

Adel Assadinia, a former career diplomat who was Iran’s consul-general in Dubai and an adviser to the Iranian foreign ministry, has claimed that Iran provides the IMN with training “in guerrilla warfare, bomb-making, use of arms such as handguns, rifles and RPGs, and the manufacturing of bombs and hand grenades.”

Assadinia, who fled Iran after whistle-blowing on corruption among the country’s all-powerful theocrats, also claimed that the IMN was set up by and modeled on Hezbollah, a Shia Islamist militant group and political party based in Lebanon.

Ibrahim Haruna Hassan, a professor in the department of religious studies at the University of Jos in Nigeria’s north-central region, wrote in his “Introduction to Islamic Movements and Modes of Thought in Nigeria” that IMN’s “stated mission is to establish an Iran type of Islamic state in Nigeria, which has kept it in intermittent skirmishes with government security forces.”

The IMN reportedly has a youth front, whose members undergo military training. But so far, these militants haven’t been a huge threat to the Nigerian state.

“They believe that the time to take up arms is not ripe in Nigeria," Hassan wrote.

The IMN have always had reasons to mount elaborate processions involving thousands of members, including women and children, trekking from one city to the other, which no one dared to disrupt before the incident that happened between the group and the army on Dec. 12.

Traffic on major roads in the north is often held to a standstill, whenever members of the movement are on such pro­cessions. Early this year, then-governor of Kaduna State, Ramalan Yero was forced to trek for a long distance after the IMN blocked the highway to motorists.

In 2012, Zakzaky told the BBC in an interview that he trained his men—running into hundreds—as guards, but likened it to “teaching karate to the boy scouts.” And despite his supporters claiming the movement is nonviolent, recent clashes with security agencies have clearly proven the contrary.

Last year, at least 33 members of the IMN—including three of Zakzaky’s sons —were killed by the Nigerian army when fights broke out during a Shia procession.

Although Nigeria’s Muslim population, estimated at 60 million, is largely Sunni, the Shia minority is significant. There are no actual statistics, but some sources estimate the number to be between 4 million and 10 million followers of Shia Islam. The movement is especially strong in northeast Nigeria, the area where Boko Haram operates.

In 2007, there was tension in Sokoto state in the northwest after an anti-Shia imam, Umaru Danmaishiyya was assassinated by unknown men. Then-governor Aliyu Wamako, a Sunni, was accused of deliberately limiting the spread of Shi’ism in Sokoto, especially when the government launched an assault on Shia groups which culminated in the destruction of their headquarters.

Since then, Boko Haram has become a ruthless Sunni takfiri force in the area, sworn to murder Muslim heretics, which all Shia are considered to be. Boko Haram has targeted Shia specifically in several suicide attacks, including a blast during a procession near the northern Nigerian city of Kano that killed 22 people last month.

“Nigeria,” said Iran’s foreign ministry spokesman, “is now dealing with problems arising from extremism and takfiri terrorism and we hope that in these conditions preservation of calm and national unity in battling terrorism is prioritized while rash and unconstructive measures are avoided.”

It may be a little late for that.