Fernando Alonso has taken pole position for the Hungarian Grand Prix – but the manner in which he did so sparked immediate controversy and tensions within the McLaren team.

Lewis Hamilton had set the pace throughout qualifying and was comfortably fastest after the first flying laps in Q3.

But before starting his final run Alonso appeared to wait in the McLaren pit stall for several seconds after he had been released to go, forcing team-mate Hamilton to queue behind him.

The delay meant that Hamilton was unable to get his final run in – crossing the line four seconds after the chequered flag came out – and, sure enough, he was pipped to pole by Alonso.

Team principal Ron Dennis showed his agitation and displeasure and went to speak with Alonso’s trainer.

But he refused to be drawn on what had happened when asked by ITV Sport’s Ted Kravitz whether Alonso had deliberately hindered Hamilton or if the team had told him to wait.

“This matter will be discussed in the team and then we’ll discuss it from there,” he said.

In the post-qualifying press conference, Alonso denied suggestions that he had resorted to gamesmanship.

“The team was holding me back,” he said.

“We tried to have a little bit of space to the Ferraris in front of us.”

It was a bitter disappointment for Hamilton, who was using the super-soft tyre while Alonso was on the harder compound and seemed a shoe-in for pole.

The British rookie, while diplomatic, was clearly unimpressed with what happened.

“There’s not really much to say – I think you saw what happened,” he said.

Before the pit lane shenanigans Hamilton had been in command, but Alonso’s final flier shaded him by just over 0.1s.

Nick Heidfeld took advantage of a torrid session for Ferrari to take third on the grid for BMW Sauber.

It remains to be seen whether the Hinwil-based team went for a light fuel load to give Heidfeld track position, but either way his presence on the inside of the second row will be unwelcome for Ferrari.

Last year’s Hungaroring polesitter Kimi Raikkonen will start alongside Heidfeld in fourth after lapping three-quarters of a second slower than Alonso.

But at least he fared better than team-mate Felipe Massa, who qualified 14th after a calamitous Q2.

The Brazilian had just left the pits for his second run of the session when he was informed that he did not have enough fuel on board.

He stopped the car in the pit lane and was wheeled back into the garage, and although he got back out in time for a final attempt, he was visibly struggling for front-end grip and missed the cut for the pole shoot-out.

Nico Rosberg took advantage of Massa’s travails to qualify a fine fifth, having shown promising pace all weekend.

Ralf Schumacher did a good job to take sixth for Toyota ahead of the second BMW of Robert Kubica, who has been less happy with his car on Saturday than team-mate Heidfeld.

Giancarlo Fisichella was eighth in the quicker of the Renaults, surprisingly getting the better of Heikki Kovalainen who has been quicker than him all weekend but missed the cut for Q3.

Jarno Trulli (Toyota) and Mark Webber (Red Bull) will share the fifth row, while David Coulthard will line up 11th in the sister RB3.

Anthony Davidson did well to haul his Super Aguri into Q2 and qualify 15th – while both works Hondas fell at the first hurdle.