Adam Price said a "mess" over the next Welsh rail franchise and the Circuit of Wales showed Mr Skates could no longer handle his "wide-ranging brief".
Mr Price said a new cabinet secretary for transport position was needed.
Ministers accused Plaid Cymru of playing "political games" with the rail situation for its "own narrow ends".
A row has erupted between the Welsh and UK governments over the future of the rail network in Wales, with UK ministers threatening to put bids for the Wales and Borders franchise on hold.
In June, the Welsh Government decided not to offer a Â£210m guarantee to the proposed Circuit of Wales racetrack near Ebbw Vale, six years after the plans were first announced.
Mr Price, Plaid Cymru's economy spokesman, said: "From the Circuit of Wales to what looks like a billion pound blunder in procuring Wales' next rail franchise, it's clear that Ken Skates' department can no longer handle its wide-ranging brief."
His department should be stripped of its transport element "for the sake of Welsh finances and the rail services that people rely on every day", the Plaid AM said.
First Minister Carwyn Jones had "no option other than to create a new cabinet level transport secretary to clean up the mess that has been created", Mr Price added.
A spokesman for Mr Skates criticised Plaid Cymru's approach to the rail row.
"It is disappointing that Plaid Cymru seem content to use an important situation like this to play political games and exploit a situation for their own narrow ends," he said.
"Our efforts will be focused on standing up for Wales and fighting for the investment our passengers deserve."
Welsh Economy and Infrastructure Secretary Ken Skates should lose responsibility for transport, a senior Plaid Cymru AM has said.