The row broke out after staff from institutions across the UK took part in industrial action to protest over a 1% pay offer.
Members of the UCU union have organised three two-hour walk-outs over the next few weeks, with the first taking place yesterday.
The majority of Scottish universities have agreed to dock staff two hours' pay for the protest.
But the universities of Aberdeen, Dundee, Glasgow Caledonian, Robert Gordon, Stirling and West of Scotland will take a full day's pay back after ruling the strike amounted to "partial performance" - and was therefore a breach of contract.
The union argues the response is against the law and has threatened legal action. It is also angry after it emerged earlier this week that a number of university principals have accepted inflation-busting pay rises.
Mary Senior, UCU Scotland official, also believes the move to cut pay is counterproductive because it could lead to a longer period of disruption for students.
"It is particularly disappointing that Scotland is leading the way in terms of threatening to dock staff pay," she said.
"Such a punitive and intimidating approach from principals can only harm Scotland's reputation for fair play and academic excellence."
The row comes just days after Scottish university principals were accused of hypocrisy and greed over their own pay rises, with an average increase of more than 4% in 2012/13.
The UCU said it would be taking legal action to force universities to pay the full amount owed to lecturers.
However, the Scottish universities who have decided to dock a full day's pay defended the move.
A spokesman for Stirling University said: "We regard participation in strike action by members of the UCU as partial performance and a breach of contract and, consistent with legal advice given to the sector employers' association, and from our own legal advisers, will deduct a full day's pay."
UCU is embroiled in a pay dispute with UK universities after university bosses refused to improve a 1% pay offer that they say will leave staff with a real-terms 13% pay cut since 2009.
Union members took two days of strike action last year and have warned of more industrial action to come if the employers refuse to come back to the negotiating table with a fairer pay offer. Student groups have described the employers' offer as "measly".
The Universities and Colleges Employers Association, which negotiates pay for all UK universities, argues the offer is the best that can be afforded in the financial climate. They also stress that staff not yet at the top of pay scales will receive a 4% pay increase due to established incremental rises.