Health minister Ann Keen and her husband, MP Alan Keen, were in breach of the rules of the House in continuing to make claims on their second home.
In a memorandum to the standards and privileges committee, the parliamentary commissioner for standards said the Keens were guilty of "a serious breach of the rules involving significant public funds".
John Lyon, the commissioner, said they should pay back more than £5,000 or four months worth of claims.
The committee decided they should repay just £1,500 citing the "exceptional circumstances" of the case.
Ann Keen has been MP for Brentford and Isleworth since 1997 and Alan Keen has been MP for the neighbouring constituency of Feltham and Heston since 1992.
The couple claimed for a second home in Brentford that was uninhabitable from June 2009 to October 2009. The property was later occupied by squatters.
The commissioner, John Lyon, concluded Mr and Mrs Keen were in breach of the rules of the House in continuing to identify their property in Brentford as their main home "when they were unable to live in it from December 2008 to October 2009 because of building work on the property which had gone wrong".
By continuing to treat their Brentford home as their main home during this period they were able to continue to claim against their parliamentary allowances for their flat in central London.
"Were the (standards and privileges) committee not to accept this conclusion, I conclude that Mr and Mrs Keen were nevertheless in breach of the rules of the House in receiving a personal financial benefit from the claims which they made for their London flat from December 2008 to October 2009," Lyon said.
"This was because they stayed overnight in the flat for four additional nights a week when Parliament was sitting and six additional nights a week in the recess.
"These were nights which they would otherwise have spent in their Brentford home and which, without the London flat and in the absence of their Brentford house, they would have had to fund from their own resources."
Lyon added that the Keens "clearly both believed that it should have been permissible for them to continue to claim in full on their London property because they still saw Brentford as their main home.
"They were reinforced in this view when the House authorities agreed that their claims could continue to be met. And it did not seem to occur to either of them (or indeed to the parliamentary authorities) that Mr and Mrs Keen's use of their publicly-funded second home in place of their Brentford property gave them a personal financial benefit."
The committee said: "We conclude that Mr and Mrs Keen were in breach of the rules of the House because for a period of four months they claimed allowances for a second home when they only had one home available to them.
"This breach is significantly mitigated in our view by the approval given by the Department of Resources, by the lack of any evidence that Mr and Mrs Keen intended to procure for themselves a personal benefit, and by very difficult circumstances beyond their control."
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