Pakistan’s central bank governor has stepped down citing “personal reasons,” two days before the announcement of the 2010/11 federal budget, the Finance Ministry said.

“We don’t know what the reasons are for the resignation, but the timing of it can be worrisome,” said Sayem Ali, an economist at Standard Chartered Bank. “It is right before the budget is announced and relations with the IMF are in a bit of a difficult stage.”

“There is definitely more than personal reasons to his resignation,” said a senior government official, requesting anonymity. “There were a couple of issues, and there was a tussle going on between him and the government. I cannot divulge on the issues, but I can say all was not well.”

The announcement was made at 2:41 am on June 3 in an e-mail from the Finance Ministry.

“Salim Raza, Governor, State Bank of Pakistan (SBP) submitted his resignation from the post of Governor on 6th May 2010, citing personal reasons,” the ministry statement said.

It was not immediately clear why the announcement was delayed, if he had stepped down nearly a month ago. Earlier, a source close to Raza said the government had accepted his resignation. “Yes, I can confirm he has resigned and his resignation has been accepted, but I cannot comment on the reasons for his resignation,” the source said.

Raza was appointed central bank governor in December 2008.

Although he had little direct impact on the federal budget, Pakistan’s financial institutions have been under pressure from the International Monetary Fund to make painful reforms.

Yaseen Anwar, deputy governor of the State Bank of Pakistan, has become acting governor, the Finance Ministry said.

Anwar, appointed deputy governor in March 2007, is a former executive vice president for London’s Kraken Financial Group.

Stock brokers said Raza’s resignation would have little impact on the market and they were waiting for who the next governor would be. Pakistan’s main stock exchange index opened 0.35 percent higher at 9,532.31 points.

“The resignation of the SBP governor should have no material impact on the markets especially since most policies are coordinated with donor or multilateral agencies, leaving little room for dynamism by individuals in formulating such policies,” said Asad Iqbal, chief investment officer at Faysal Asset Management Ltd.

Pakistan turned to the IMF in November 2008 for an emergency package to avert a balance of payments crisis and shore up reserves and received the fifth tranche this month amounting to $1.13bn of a $10.66bn loan.