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Fernando Santos questioned the referee's performance after Portugal suffered the first defeat of their Nations League campaign to Switzerland.
Haris Seferovic opened the scoring after just 55 seconds in Geneva, the fastest goal in Nations League history and earliest Switzerland have scored since 1988.
Referee Fran Jovic awarded a penalty to Switzerland 13 minutes later for a handball against Nuno Mendes, but the VAR overruled the decision.
A clear foul on Andre Silva by Nico Elvedi on the halfway line was the reason, with the Portugal striker requiring brief medical treatment for the ankle injury suffered in the tackle.
Portugal were incensed at the original decision, surrounding Jovic at half-time, and tempers continued to boil over in the second half, with Bruno Fernandes confronting the Swiss bench at one point.
While Santos refused to directly criticise the referee's performance, he admitted his frustrations with Switzerland seemingly slowing down the game en route to a 1-0 victory.
"I'm not going to criticise, but when a penalty is awarded that doesn't happen just like that, when there's a clear foul in midfield... Then just look at the number of fouls and time lost," he told reporters.
"The fourth official knows very well what happened in the game."
Santos was satisfied with the second-half improvement, even if Swiss goalkeeper Jonas Omlin's heroics left Portugal a point behind group leaders Spain, who defeated Czech Republic on Sunday.
"At half-time, I was just saying that we have to have the ball and play differently and push them back," he added.
"We started very well, in the first few minutes we wanted to put the ball very quickly on [Goncalo] Guedes. We knew opportunities would arise and many have arisen."
Portugal are not in action again until visiting Czech Republic in the Nations League on September 24.