Islamabad, Pakistan - The Election Commission of Pakistan has rejected the registration application of a new political party due to its links to charities said to be fronts for the armed Lashkar-e-Taiba (LeT) group.

Milli Muslim League's (MML) application for registration was rejected on Wednesday by a four-man panel headed by Chief Election Commissioner Sardar Muhammad Raza in the capital Islamabad, MML spokesperson Tabish Qayyum confirmed to Al Jazeera.

"We have been told that we need to get clearance from the interior ministry," he said. "This is an unprecedented move."

Qayyum said the MML would challenge the ECP's decision in the high court in the coming days.

The ECP's decision was based on a letter from the interior ministry advising the panel that the political party was known to be linked to the Jamaat-ud-Dawa (JuD) and Falah-e-Insaniat Foundation (FIF) charities, both of which are subjected to international anti-terrorist sanctions by the UN and US.

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According to the UN, JuD and FIF are front organisations for LeT which is blamed for carrying out attacks against Indian security forces in the disputed region of Kashmir. LeT was also blamed for the 2008 Mumbai attacks which killed 166 people.

JuD chief Hafiz Muhammad Saeed, who is also founder of the LeT, has been designated as a "terrorist" by the UN. The US has also placed a $10m bounty on Saeed for his role as JuD chief.

Saeed has been under house arrest in the eastern city of Lahore under local anti-terrorism laws since January. He denies any wrongdoing and rejects claims that the JuD and FIF have any links to the LeT.

Launched in August this year, MML officials confirmed that while the party shares ideological links and supporters with the JuD, it is a legally distinct entity that does not share any officials.

Saifullah Khalid, the MML chief, has long been a member of JuD's central leadership, although the party says he has now given up that post.

"The MML structure and design is independent - there are no office holders who are also leaders of the JuD," said Qayyum.

"They may go to events and programmes, but they are independently in the MML now, it is totally separate."

'Mainstreaming' debate

Last week, Pakistan's military spokesman confirmed that the state was working on a "mainstreaming" programme to induct members of armed groups into the political process and away from carrying out "terrorist" activities.

"It is in my knowledge that the government has started some discussion over how to mainstream them so they could do constructive contribution," Pakistan Army spokesman Major-General Asif Ghafoor told reporters at a press conference.

Ghafoor did not comment on the military's specific role in such a programme.

Last month, an MML candidate ran as an independent candidate in a major by-election in Lahore, challenging the ruling PML-N in its political heartland.

Muhammad Yaqoob Sheikh finished fourth in that election, garnering 4.6 percent of the vote. Sheikh's election banners prominently featured images of JuD chief Saeed, and several voters told Al Jazeera they were moved to vote for him based on JuD's humanitarian work across the country.

Tehreek Labbaik Pakistan, a right-wing religious party that featured images of Mumtaz Qadri, a man convicted of murdering a provincial governor over blasphemy allegations, finished in a surprising third place, with 5.6 percent of the vote.

The MML registration rejection comes days before another by-election, in the northwestern city of Peshawar, where the party is fielding its candidate as an independent.

Asad Hashim is Al Jazeera's web correspondent in Pakistan: @AsadHashim