Michael Russell, the Education Secretary, also indicated he may legislate to improve gender balance.
The Herald revealed yesterday that just 25% of members of university ruling Courts were female, despite the fact women academics make up more than half the workforce.
The figures for 2011/12, compiled by student body NUS Scotland, also show that none of the current chairs of university Courts are women.
The Post-16 Education (Scotland) Bill aims to put in place a new code of conduct for universities, which could require each governing body to ensure at least 40% of its membership is female.
Mr Russell, giving evidence on the Bill, said: "I do think there is room for improvement. I will consider whether an amendment should be laid to take that further.
"I know there is the suggestion that there should be a proportion or a percentage and I will actively consider that.
"It is stark, the situation that we have. I think it is alarming that we are still in that situation."
Earlier, Mr Russell denied the Bill gave more power to ministers, arguing it underpinned good governance, rather than interfering.
He also stressed the importance of a cap on fees charged by Scottish universities to students from the rest of the UK.
Last week, the Committee of Scottish Chairs called for the cap to be scrapped, allowing universities to set fees.
Liz Smith, education spokeswoman for the Scottish Conservatives, said: "This Bill is a mess. It is badly constructed and seems set to create only more confusion.
Scottish LibDem leader Willie Rennie said: "Mr Russell must resist his natural temptation to meddle and reconsider how best the Government can achieve the improvements we all want to see."
Scottish Labour MSP Neil Findlay, added: "There is a real lack of clarity about the purpose, benefits and scope of this Bill."
Mary Senior, Scottish official of the UCU lecturers union said: "Legislation is required to compel universities to do more on widening access."