BEIRUT/AMMAN (Reuters) - Military sites in Syria are packed with soldiers who have been effectively imprisoned by their superiors due to doubts about their loyalty, ex-soldiers say, making them possible casualties in any U.S.-led air strikes.

U.S. President Barack Obama speaks during a meeting with Baltic leaders in the Cabinet Room of the White House in Washington August 30, 2013. REUTERS/Kevin Lamarque

Thousands of loyal security forces and militia, meanwhile, have moved into schools and residential buildings in Damascus, mixing with the civilian population in the hope of escaping a Western strike, according to residents and opposition activists.

U.S. President Barack Obama says a “tailored, limited” strike would send a strong message to Syrian President Bashar al-Assad that use of chemical weapons cannot be tolerated after an alleged attack last week killed hundreds of people.

Officials in Washington, rejecting comparisons with the 2003 U.S.-led invasion of Iraq, say any campaign would likely include cruise missiles from U.S. ships in the Mediterranean, last only days and target military installations including air defenses.

They may, however, involve casualties among the Sunni Muslim majority that has led the revolt against Assad.

Some military and security bases are used as prisons for civilian detainees, human rights groups say, and rebels who have fled their posts say many soldiers of a low rank are imprisoned on military sites because they are Sunnis.

Most of the commanding officers are from Assad’s Alawite sect, an off-shoot of Shi’ite Islam, and fear their subordinates will defect, flee their posts or coordinate with rebel units, defectors say.

“Some soldiers are physically locked up in rooms and others are given small jobs to do around the base but their weapons are taken from them. They are not taken out of the base,” said an ex-soldier who, until three months ago, worked at an artillery base on the outskirts of Damascus.

He said he was able to flee his post after he became ill and was taken to hospital, where he escaped and hoped his superiors would not report his disappearance due to the chaos of war.

The man, who spoke by telephone, asked to remain anonymous to protect his family who live in government-held territory. He said that trapped soldiers would likely die in military strikes.

Also asking to remain anonymous, a rebel from the northern province of Idlib said his unit was allowed to exit the barracks to fight on the frontlines of Aleppo, but under duress and the threat of execution for desertion.

“One day I was fighting and I was separated from my unit. The revolutionaries called out to me and I crossed over to them.”

“I am worried that the strikes will hit the imprisoned soldiers,” he said, but added that he also hoped a strike on Assad’s military would prevent further deaths.

One former senior U.S. official said reports of Syrian soldiers being held by their superiors as possible human shields underscored the importance of choosing the appropriate targets for cruise missile strikes.

“It is a really hard problem,” said the former official. “Any strikes will be claimed by the regime to have killed innocents or the wrong people.”

IMPRISONMENT

Since civil war broke out in 2011, conscripts have no longer been allowed to take annual leave and their two-year military service has been extended indefinitely, defectors say.

The army would rather incur the cost of imprisoning Sunni soldiers than run the risk of defection, say rebels, who estimate thousands of Syrian Sunnis are held at military sites.

Many talk of a brother, friend or family member who has not been heard from and is suspected of being trapped.

It was not clear whether the bases where they say soldiers are held included possible U.S. targets, and Pentagon officials were not immediately available for comment. The U.S. military says it works hard to avoid civilian and unintended casualties.

Opposition activists say that in anticipation of U.S. strikes, the army has started moving personnel and military equipment, including Scud missiles, to protect supplies.

Many of those working in secret police compounds that dominate the capital have also moved - into schools and civilian buildings, residents, diplomats and opposition activists said.

A woman living in the western Kfar Souseh district, which is home to Military Intelligence and other security compounds, said security personnel armed with AK-47s rifles and carrying radios had taken up residence in the basement of her apartment bloc.

“They are loudly playing the song ‘We Are Your Army Bashar,’” she said. “Imagine if you are living somewhere for years and 60 gunmen you don’t know suddenly barge into your building and live there,” she said.

Activist Moaz al-Shami, who is compiling a list of schools where security and pro-Assad militia have moved in, said they concentrated in Baramkeh, Tishreen Park, Sha’lan, Abu Rummaneh, Mezze and Malki, among the most heavily fortified districts of the capital and home to many top army and intelligence officers.

“If those schools get hit the risk to civilians around them could be greater and the regime can accuse the United States of indiscriminate bombing and targeting civilians,” Shami said.

Diplomats said rebel raids and fighting near key roads had blocked a wider evacuation of the hundreds of security and army bases that dot the country of 22 million, where Assad’s late father imposed his autocratic dynasty four decades ago.

Khaled Saleh, a spokesman for the opposition Syrian National Coalition, said as well as personnel movements out of military sites, prisoners had been put in barracks as human shields.

“The Assad regime is starting to move large numbers of prisoners into army barracks. Over the last three days, they are moving soldiers into schools and hospitals,” he said in Istanbul.

Reuters cannot independently confirm Saleh’s report, which he says is based on eyewitness accounts, or those of the ex-soldiers, due to security and reporting restrictions in Syria. Attempts to reach Syrian officials for comment on this story were unsuccessful.

Peter Splinter, Amnesty International’s representative to the U.N. in Geneva, said his rights group did not have confirmation prisoners were being moved but was very concerned about thousands of detainees already in military and security bases that may be targeted.

He said authorities had partly transformed some military bases into detention facilities since the start of the uprising because of the large number of arrests.

The conflict started with a peaceful pro-democracy movement against four decades of Assad family rule but became armed after a crackdown by security forces. Attacks have included incendiary and cluster bombs, as well as summary executions, and the United Nations says 100,000 people have been killed.