Formula One bosses are investigating McLaren for a possible breach of the rules in Sunday's Monaco Grand Prix.
Alonso (right) beat Hamilton in Sunday's race
McLaren team boss Ron Dennis admitted he prevented Britain's Lewis Hamilton challenging eventual winner Fernando Alonso after their first pit stops.
A statement read: "The FIA has launched an investigation into incidents involving the McLaren Mercedes team."
McLaren denied using team orders, which have been banned since 2002, but said they had employed team strategy.
The FIA is investigating a possible breach of the international sporting code.
The code states it will punish "any fraudulent conduct or any act prejudicial to the interests of any competition or to the interests of motor sport generally".
But a McLaren spokesman insisted: "We are very confident about FIA's investigation into our race strategy.
We do not, and have not, manipulated Grands Prix unless there are some exceptional circumstances
McLaren team boss Ron Dennis
"All the decisions that we took before and during the race respect perfectly the international sporting code."
At a post-race news conference Dennis admitted he "virtually had to decide in advance" which driver would win because of the challenging nature of the tight street circuit.
Hamilton was hoping to claim his maiden Formula One victory and extend his lead over Alonso in the drivers' championship.
But the 22-year-old was instructed "to take it easy" late on after he closed to within 0.8 seconds of the double world champion.
That left the Spaniard clear to take his second victory of the season 4.095 seconds ahead of his young title rival but left Hamilton bemoaning his second fiddle role.
However, Dennis said he had a clear conscience and insisted there was nothing wrong with his plans for the 78-lap race.
"Team strategy is what you bring to bear to win a Grand Prix; team orders are what you bring to bear to manipulate a Grand Prix," he said.
"We do not, and have not, manipulated Grands Prix unless there are some exceptional circumstances."
Dennis also denied favouring Alonso over Hamilton.
"Lewis and Fernando enjoy being in a competitive team and having competitive cars," he added.
"But one of the things you have to come to accept is that if you are a member of this Grand Prix team, for the vast majority of the time, there is equal opportunity for drivers to race. But Monaco is not one of them.
"Our job is to win races and win world championships," insisted Dennis.
"That rarely, but occasionally, comes before having to allow the drivers to race."
An FIA spokesman declined to say what possible sanction might be faced by the team, who lead Ferrari by 20 points in the championship.
Alonso leads the drivers' standings on 38 points, the same number as Hamilton, but has the edge because he has won two races.