His fire was aimed at the Union Connectivity Review, which was announced by the UK Government in June.
It is thought the Department for Transport-commissioned review will examine potential projects such as a link between Scotland and Northern Ireland, and extending the Borders Railway south to Carlisle.
It will conduct a “detailed initial assessment of options for improved road and rail connections between England and Scotland, and England and Wales, as well as improved air links across the UK”.
The review, led by Network Rail chair Sir Peter Hendy, is due to report next summer.
Asked by South Scotland Conservative MSP Michelle Ballantyne whether the Scottish Government would be taking part, Mr Matheson said: "The Union Connectivity Review was set up without any consultation with the Scottish, Welsh or Northern Irish governments.
"Its remit and chair was decided by the UK Government without any engagement with the devolved governments.
"It is going to make recommendations, in areas which are the responsibility of this Parliament [Holyrood], directly to UK ministers.
"It is nothing more than a blatant power grab, and an attempt to over reach the powers of this Parliament.
"We have a very clear process for deciding what infrastructure, and in particular transport priorities are in Scotland, and that includes looking at cross-Border connectivity."
Mr Matheson said the other devolved governments had also expressed concerns.
However, the Department for Transport (DfT) disputed his comments.
A spokesperson said: “This is untrue and the devolved governments were consulted by ministers ahead of the review.
“The UK Government is well placed to level up transport infrastructure and improve connectivity between Scotland, Wales, Northern Ireland and England, boosting access to opportunities and improving people’s everyday connections.”
“The review is firmly focused on improving connectivity for citizens across the UK and Sir Peter Hendy will engage with the devolved administrations throughout the review period.”
The DfT said the review would also seek the views of transport operators, business and academics “to ensure a wide range of representation”.