But the merger would restrict academic freedom to institutional level rather than extend it to individual FE lecturers - despite union representations.
Jim Wallace, Minister for Enterprise and Lifelong Learning, opened the parliamentary debate on stage one of the Further and Higher Education (Scotland) Bill, saying: "The bill extends academic freedom at an institutional level from higher education to the college sector.
"I share the belief that academics in both sectors should be free to challenge received wisdom and to express controversial or unpopular opinions, and I welcome the opportunity to state in the strongest terms that that freedom of expression should exist in all institutions. The issue is important and extending academic freedom to colleges sends a strong message on the maturity and importance of the sector, but individual freedom is primarily a matter between the institutions and their employees.
"Since the issue was raised, I have received a number of representations, including some from those who point out that the issue is already covered in some contracts," said Mr Wallace.
The committee heard from the Educational Institute of Scotland and the Association of University Teachers that individual academic freedom should be extended to cover all institutions.
Lord Watson, Labour MSP for Glasgow Cathcart, suggested that academic freedom for individuals could be built into the bill and said he hoped that could be investigated at Stage 2.
Mr Wallace promised to consider the matter further but "outwith the Bill process".
Murdo Fraser, for the Conservatives, called for the new funding council to consider setting up a skills committee as "an early priority" to complement the new council's research committee, which would be statutory.
Mr Fraser said a skills committee would be relevant to the work of the funding council, particularly in connection with further education, but it would also offer parity of esteem.
"It is inevitable that a research committee will deal primarily with the higher education sector," he said. "Therefore, it makes sense to have a skills committee to deal primarily with the further education sector.
"That would create a balance and ensure that those who run the funding council treat both sectors equally."