The total cost of five key schemes has increased by Â£379 million to more than Â£1.5 billion, a Scottish Government-commissioned report showed.
Improvements to the Aberdeen-Inverness line and electrification of the secondary Edinburgh-Glasgow line via Shotts are now expected to cost twice as much as expected.
The cost electrifying the Edinburgh-Glasgow main line via Falkirk has increased by Â£136m to Â£795m.
The report said costs of the projects had increased "very sharply" in a short time.
It attributed these to significant underestimates of the cost of the work, failure to meet regulations and poor knowledge of existing infrastructure.
Mr Yousaf told MSPs today he was "astounded" at the lack of Holyrood control of Network Rail over delays to major projects like the Edinburgh-Glasgow main line electrification.
He called for the full devolution of powers over the the UK Government body to the Scottish Parliament.
Mr Yousaf was expressing his frustration at delays to the upgrading schemes, with completion of the main line electrification project being put back from December to July next year.
Upgrading the Aberdeen-Inverness line has nearly doubled from Â£170m to Â£330m, electrification of the Edinburgh-Glasgow line via Shotts doubled to Â£160m, and electrification of lines to Dunblane and Alloa increased by Â£55m from Â£105m to Â£160m, or by about 50 per cent
However, improvements to the Perth-Inverness route will now cost Â£65m rather than the forecast Â£117m, a saving of about 50 per cent, because different trains will be used on the line by ScotRail than originally planned.
Mr Yousaf told the rural affairs and connectivity committee: "I'm astounded at the lack of leverage and control the Scottish Parliament has over Network Rail.
"I do not feel that is an acceptable situation whatsoever.
"[Scottish Government agency] Transport Scotland lacks effective leverage."
Mr Yousaf also criticised Network Rail, which is responsible for infrastructure such as tracks, for failing to keep the agency informed of problems.
He said: "What frustrates us is the delay in information from Network Rail, coming far too late in the day to Transport Scotland to be able to act on it."
In July, the minister said he was "very concerned and disappointed" that projects would run late and could increase in cost.
The project cost increases come in stark contrast to Network Rail's previous good record in Scotland for major schemes, with construction of the Borders Railway, Airdrie-Bathgate line and the overhaul of Waverley Station in Edinburgh being completed on time and budget.
In 2004, Holyrood gained more control over Network Rail projects in the biggest transfer of powers since devolution six years earlier, as The Scotsman revealed at the time.
Network Rail said it had already acted on recommendations in a report on the delays by accountants Ernst & Young.
Karl Budge, its regional director for infrastructure projects in Scotland, said: “Prior to this report being commissioned, we introduced an improvement plan for the way in which all major projects are managed and the way in which we report progress to Transport Scotland and our regulator, the Office of Road and Rail.
“These changes directly address the recommendations that are included in the Ernst & Young report.
"We have strengthened the programme leadership team, we have established new portfolio boards and project management offices, and we have bolstered the project management teams so there is more resource dedicated to risk management and scheduling the way in which we calculate and declare project cost estimates.”