Ken Gibb, professor in housing economics and director for public policy at Glasgow University, said an evictions amnesty adopted by some councils could send the message that some arrears were not as important as others.
The focus on the bedroom tax could also be marginalising others with unrelated financial problems, he told Holyrood's Welfare Reform Committee.
Labour and the SNP have both committed to a no-evictions policy at council level but the Scottish Government has resisted calls from Labour and campaigners for a statutory ban.
Professor Gibb, who was commissioned by the committee to assess the impact of the benefit changes, said: "There needs to be some caution if one was to consider either blanket forgiveness of arrears or ruling out completely evictions."
North Lanarkshire Council, Scotland's biggest council landlord and an early adopter of a no-evictions policy, was singled out at the committee for accumulating one of the highest bedroom-tax related rent deficits in Scotland. It has £675,000 of rent arrears which may be the result of the benefit changes, according to figures compiled by BBC Scotland.
Conservative MSP Alex Johnstone said: "North Lanarkshire came out early and said there would be no evictions as a result of the bedroom tax, and then subsequently announced substantial levels of non-payment and rent arrears. Do you think the two things are related?"
Mr Gibb said: "They may well be, although I think there is evidence from other councils where I don't think that's the case.
"I do have some concerns about simply saying, in a sense, that there is a class of arrears that doesn't matter as much as other arrears.
"I worry about that in the longer term, particularly with the roll-out of universal credit and the end of direct payments. I think we should be cautious and think about the implications of that."
Deputy convener Jamie Hepburn, SNP MSP for Cumbernauld, said: "I have to assert my own perspective as to how early they announced their no-evictions policy."
Mr Johnstone suggested North Lanarkshire had not been making full use of discretionary housing payments (DHPs), money allocated by the UK Government to help people manage benefit changes.
Convener Michael McMahon, Labour MSP for Bellshill in North Lanarkshire, said the council "has maximised the amount it can put forward for discretionary housing payments".
Mr Johnstone said: "In North Lanarkshire, there seemed to be a very quick rise in arrears but a very low take-up in the DHPs and other resources to alleviate that problem.
"Do you think the political environment in North Lanarkshire in the early part of this year had some influence on the fact that some people decided to go into arrears rather than seek the assistance available?"
Mr Gibb said: "I would have been cautious about moving towards the commitments they have, for the reasons I have suggested. I also think it's important in relation to the other people, not just working-age social tenants who may be having problems in the current welfare reform environment."
North Lanarkshire Council leader Jim McCabe said welcomed the debate, adding: "I'm proud to say that this council has taken a principled stance.
"We will not evict people in this financial year whose arrears are solely due to bedroom tax and who work with us to mitigate the impacts."
l Three single mothers and their children plan to appeal a ruling yesterday at the High Court in London that Work and Pensions Secretary Iain Duncan Smith's benefit cap is lawful.