Islamabad: A day after Pakistan's Ministry of Defence surprised everyone by writing to the Supreme Court that that the Army and the ISI was not under its control, the government seems to be washing its hands off the matter.

A top official of the Federal government on Friday disowned a controversial reply filed by the ministry of defence (MoD) submitted to the Supreme Court late on Thursday.

The reply submitted on behalf of the secretary of the Ministry of Defence created a stir by stating that the Army and the ISI was not under its control.

The Secretary's reply also stated that the Ministry could not submit any reply on behalf of the Army or ISI.

However, the unnamed official told that they didn't know on whose instructions the Defence Secretary was acting – but it wasn't the federal government.

Had the government intended to submit a reply, it would have done it on its own instead of routing it through the MoD, they said.

Besides, he said, the reply should have been forwarded to the Supreme Court through the Ministry of Law, Justice and Parliamentary Affairs or the office of the Attorney General of Pakistan – which it wasn't.

Earlier, the Attorney General's office had submitted the replies of the Ministry of Interior and Ministry of Foreign Affairs to the Supreme Court.

In both the replies, the ministries reflected the federal government's stance: dismiss the petitions against the memogate affair.

The official said the Ministry Secretary did not need to refer to the filing of the replies of the ISI and the Army because it was not under the court order to furnish such replies.

He added that the court had asked only the federal government, US businessman Mansoor Ijaz and former Ambassador to the US Hussain Haqqani to "accept or deny" the replies filed by the army chief Gen Ashfaq Pervaiz Kayani, ISI DG General Ahmed Shuja Pasha and others, the report said.