The forward was sent off for a dangerous tackle while playing for Exeter Chiefs in last weekend’s 20-19 victory over Sale Sharks.
Scotland who will face Romania and Georgia in July, are not planning to call up a replacement at this stage.
Mike Blair, the national side’s interim head coach, said: “We’re disappointed that Sam will miss out on the matches this summer as we know he was looking forward to it and has been playing well at Exeter.
“Although Sam will not be directly replaced, his absence will give someone else the opportunity to step up within the squad and prove themselves.”
Skinner’s ban means he is suspended for the Gallagher Premiership play-off semi-final, also against Sale, at Sandy Park on Saturday.
He would miss the Premiership final at Twickenham on June 26 if Exeter beat Sale.
Skinner’s club-mate Dave Ewers was also given a four-week ban after being cited following his yellow card for a dangerous tackle in the same game.
The RFU said that both players contested the charges, but they were upheld by the disciplinary panel.
In a statement, the panel said: “Both cases involved direct contact with an opponent’s head that carried a high degree of danger.
“None of the mitigating factors set out in the World Rugby Head Contact Process which would have justified the red card otherwise being reduced to a yellow card were present.
“Neither player accepted the charge and so full mitigation credit was not available to them.”
It is a major setback for Exeter, who are bidding to reach a sixth successive Premiership final.