Last week, the Supreme Court ordered the arrest of Prime Minister Raja Pervez Ashraf in connection with a corruption investigation that dates back to energy projects commissioned when he was water and power minister.
The second case relates to the former head of the oil and gas regulatory authority, Tauqir Sadiq, who fled abroad after being accused of embezzling 83 billion rupees ($850 million) in kickbacks and commissions.
Members of the government accuse the court of waging a politically motivated witch hunt against the administration, which in March 2013 will become the first elected civilian government in Pakistan to complete a full term in office.
Last June the court sacked Ashraf's predecessor for contempt over his refusal to ask Switzerland to reopen corruption cases against President Asif Ali Zardari on the grounds that he has immunity as head of state.
The court in 2011 declared Sadiq's appointment illegal on the grounds that he was not qualified. It ordered the National Accountability Bureau, an anti-corruption watchdog, to investigate him on suspicion of corruption.
The NAB reported back that Sadiq was appointed by Ashraf, then water and power minister, in 2009 and allegedly embezzled 83 billion rupees.
In October 2012 the Supreme Court ordered Sadiq's arrest.
But despite being on a government blacklist, Sadiq fled the country, allegedly with the help of Interior Minister Rehman Malik and Jehangir Badar, a relative and senior member of the ruling Pakistan People's Party.
"Why hasn't NAB taken any action?" Judge Jawwad Khawaja asked NAB officials in court on Thursday. NAB officials asked the court for an extra week.
"File references against all those involved, including the minister and other government functionaries who appointed Tauqir Sadiq and all those who facilitated his escape, before January 31," Khawaja said.