A Pakistani anti-corruption court on Thursday issued a non-bailable arrest warrant against former prime minister Yousaf Raza Gilani in a case alleging millions of dollars of corruption in a trade development scheme, a security official said.

The same day, another senior figure in the opposition Pakistan People's Party (PPP) was accused in court of financing terrorism after being arrested the previous day. The PPP accuses its enemies of waging a smear campaign through the courts.

Gilani was prime minister in the PPP government from March 2008 until his disqualification and ouster by the Supreme Court of Pakistan in April 2012. He is currently vice chairman of his party.

The warrant was issued for Gilani and another senior party leader, Makhdoom Amin Fahim, according to Javed Akbar Riaz, an official with the Anti-Corruption Unit of the Federal Investigation Agency.

The pair was ordered to appear before the court on 10 September.

Riaz said the agency had petitioned the court for the prosecution of Gilani and Fahim over their alleged approval and disbursement of hundreds of millions of dollars to fake companies through the government Trade and Development Authority.

PPP Senator Sherry Rehman said the charges were politically motivated.

"It seems a revenge-like campaign is being carried out against the PPP," Sherry Rehman told a news conference.

Another prominent PPP figure appeared before an anti-terrorism court in Karachi on Thursday and ordered to be detained for 90 days.

Court papers alleged Asim Hussain, a petroleum minister in the previous PPP-led government, had been involved in "terror and violence financing, misappropriation of funds for enhancing support for terrorism and other criminal activities".

The cases are the first of their kind against the PPP in a sweeping crackdown on violence and corruption spearheaded by the military this year.

Critics accuse the military, which has a history of launching coups, of seeking to weaken the civilian political system in place since 2008.

The military says the crackdown is necessary to break the cycle of corruption and violence in Karachi. It has so far targeted mostly opposition politicians and not the ruling party of Prime Minister Nawaz Sharif.