The Prime Minister's Office is facing a formal complaint that it is in contempt of Parliament for its role in a $90,000 gift to Senator Mike Duffy.

The Speaker of the Senate will be asked to rule on whether Canada's executive branch improperly interfered with the legislative branch.

The Liberal Leader in the Senate, James Cowan, is expected to make the request shortly after 6 p.m. It will be the first sitting of the Senate since two of its members – Mike Duffy and Pamela Wallin – resigned from the Conservative caucus to sit as independents in response to questions over their expenses.

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If the Speaker agrees that the PMO appears to be in contempt of Parliament, he could ask a Senate committee to review the situation and make recommendations.

Mr. Cowan is expected to argue that Nigel Wright – who resigned Sunday as Prime Minister Stephen Harper's chief of staff – improperly interfered with Parliament by secretly giving Mr. Duffy over $90,000, a move which allowed the Senator to pay back all of his expenses that were in the process of being audited. As a result of the repayment, Mr. Duffy stopped co-operating with auditors, refusing to provide documents and refusing to meet with them to answer questions.

Even though auditors reported this lack of co-operation, the Conservative government initially praised Mr. Duffy for providing leadership.

After the role of Mr. Wright in the repayment became public, Ms. LeBreton's tone changed. She is proposing to have Mr. Duffy's expenses sent back for a further review. That option is expected to be debated Tuesday evening.

The Tuesday evening sitting of the Senate will include a question period and a possible debate on the recently-released audit reports into the expenses of Mr. Duffy and Senators Patrick Brazeau and Mac Harb. Auditors continue to examine Ms. Wallin's expenses and no report has yet been released.

The Prime Minister commented generally on the controversy Tuesday morning but did not take any questions from the media.

"I don't think any of you are going to be very surprised to hear that I'm not happy, I'm very upset about some conduct we have witnessed – the conduct of some parliamentarians and the conduct of my own office," said Mr. Harper.

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Mr. Harper was not in the House of Commons for Question Period Tuesday as he is travelling to Peru.

Foreign Affairs Minister John Baird answered on behalf of the government. He said the Prime Minister was not aware of the payment to Mr. Duffy.

"The Prime Minister was not aware of this payment until media reports surfaced last week," said Mr. Baird. The minister noted that the payment is now being reviewed by the federal Ethics Commissioner. He also said there was no written agreement between Mr. Wright and Mr. Duffy.

An earlier version of this story stated that government cabinet ministers, inlcluding Marjory LeBreton, the Government Leader in the Senate, initially praised Mr. Duffy for providing leadership. In fact, Ms. LeBreton did not use the term leadership. The word "leadership" was used by Government House Leader Peter Van Loan.