Newcastle's opening pre-season friendly at Darlington was marred by two pitch invasions on Friday night.
Joey Barton put United ahead after two minutes before Sammy Ameobi doubled the lead, 10 minutes into the second half.
Newcastle fans then invaded the field at the Darlington Arena with Barton and team-mate Alan Smith urging them to return to the away end.
But when the match restarted, fans flooded back on to the pitch forcing another delay.
The pitch was again cleared, with Newcastle manager Alan Pardew and assistant manager John Carver walking over to the club's supporters to urge them to calm down.
Newcastle went on to win 2-0 although the result was overshadowed by the disruptions which led to the arrest of three fans for pitch incursion.
"On behalf of everyone at Newcastle United FC, we wholly condemn the behaviour of a number of our supporters who invaded the pitch during the second half of the club's friendly against Darlington this evening," the club's managing director Derek Llambias said in a statement on the club's website.
"The club will be seeking to obtain footage of the disorder from Darlington FC and the police and will be taking the strongest possible action against those individuals responsible for the shameful behaviour.
"This behaviour is not typical of the vast majority of our fans, however this incident gives a poor impression of Newcastle United and its loyal supporters."
Speaking on BBC Radio 5 live, Pardew added: "It was unfortunate because what seemed to be a jovial kind of chant went up about if Sammy scored, and he did.
From that there was a pitch invasion. Of course you don't want it but it seemed in good heart.
"Somewhere along the line it got lost and there were a couple of nasty incidents on the pitch.
"The majority were excellent but it's a shame. We've tarnished the game where we've performed very well."