MacDonald couldn't be reached for comment, but in a letter to legislature Speaker Gordie Gosse he offers to make donations to two charities in Cape Breton because of his absence from the house.
"These contributions would be equal and based on the anticipated financial reimbursement decision of the legislature management commission," wrote MacDonald.
The commission was scheduled to meet Thursday to discuss MacDonald's case. It was expected to decide whether he would have to repay some of his salary for being absent.
MacDonald represented the riding of Cape Breton South for 20 years, but found himself at the centre of a controversy when he took vacation time in April.
He has previously told media outlets he booked the vacation believing that an election would be underway.
MacDonald had decided not to seek re-election and Liberal Leader Stephen McNeil has said he declined attempts by MacDonald to resign last fall and again this spring.
McNeil said he had no regrets about his previous decisions despite attempts by the NDP and Progressive Conservatives on Wednesday to blame him for a lack of leadership in handling MacDonald's situation.
"Manning has been contributing to our party and to our caucus up until today," said McNeil. "If I made a mistake it was judging the fact that we may have had a general election before now."
McNeil said with MacDonald's retirement, the Liberals will ask the Speaker to reduce the party's caucus budget because it will be operating with one fewer member.
Meanwhile, deputy premier Frank Corbett said Wednesday that MacDonald's retirement doesn't change his intention to move a motion dealing with his vacation absence before the management commission
"The reality is we think this was a move by the Liberal party to pre-empt the committee in investigating this any further," he said.
Corbett said while the commission would now have to consider what MacDonald and the Liberals are suggesting, he would still recommend looking at docking MacDonald's pay for each day he was away.
In an earlier interview, Corbett alleged that MacDonald violated house rules because he didn't get the permission from the Speaker to leave for an extended period. Under the legislature's rules, the commission has the right to levy a penalty, although the exact nature of the sanction isn't specified.
Liberal Andrew Younger, who is on the commission, said although he wouldn't be defending MacDonald's absence, his party believes there should be an examination of all members' attendance.
He said there have been times when legislature members from other parties have been absent because they were on vacation.
"If we are going to levy a financial reimbursement against Manning then obviously we are imposing conditions on a rule that will have to be applied equally to all members," said Younger.
He said the rules around attendance also need to be clarified.
"Lets figure out what the rules should be and how we should deal with it," Younger said.
Gosse didn't rule out the possibility of updating the rules but he said it could prove difficult to get all three parties to agree, given that previous attempts to tweak some of the proceedings of the house have failed.
He said MacDonald told him he was tired and needed a break from the house.
Gosse wouldn't speculate on whether MacDonald thought he had complied with the rules.
"I don't know what he understood because he didn't ask for permission," said Gosse.
Chris d'Entremont, the lone Progressive Conservative member of the commission, said he would support any government move to penalize MacDonald because the public has expectations of its politicians.
"Part of our job during house sittings is to be in our seats to bring the issues and thoughts of our constituents forward," he said. "Mr. MacDonald didn't do that."
In addition to the Speaker, the management commission consists of four government members, two Liberals and one Progressive Conservative.