Keith Brown defended the electrification programme which now includes the full scale redevelopment of Queen Street Station, as critics said it was delayed and had increased in cost.
The plan is to run longer trains on the line, which will be electrified to reduce the journey time to 42 minutes and rebuild Queen Street Station, linking it to Buchanan Galleries.
Last week Transport Scotland produced the Final Business Case for the Edinburgh to Glasgow Improvement Programme (EGIP) and the final cost of £742m.
It was criticised as being delayed and questions on the impact on other services during construction and after, remain to be answered.
Mr Brown faced questions from three MSPs in the Scottish Parliament. He was asked by Neil Bibby, West of Scotland Labour MSP, what the impact would be on services during the construction phase.
Sarah Boyak, Labour MSP, asked why the business case took so long to be published, and Annabel Goldie, Tory MSP asked if there were any other plans to improve services between the cities.
Mr Brown said the work was necessary and the cost increase was to allow Queen Street to be redeveloped, and he admitted disruption was inevitable.
He said: "I have provided information in the past how it being managed. There will be use of buses and work is ongoing to minimise the disruption, which is inevitable.
"We are going to have improvements much of which should have been done decades ago."
He said the Final Business Case was published at the earliest opportunity in January which he said was consistent with the recommendations of Audit Scotland.
Ms Boyack said the project was unrecognisable from its original intention and claimed costs were up.
Mr Brown rejected the claim and said the project, like all others, had to be seen in the context of a cut in the capital budget of 26%
He said when the cost was cut from £1.2bn to £650m, he was urged to spend more, and said the electrification costs had been reduced by £50m, allowing for the Queen Street plan to be included.
He said: Capital works of £742m is a very good thing. Much of this is being done because it wasn't done previously."
"We had the UK Transport Minister Patrick McLaughlin coming to Scotland to say the same. We are cracking on with projects that should been done years ago."