"I am extremely disappointed that I will be unable to play in the US Open," the 43-year-old Northern Irishman said in a statement released by his management team on Monday.
"But I have to make sure I am 100 per cent ready for The Open at Royal Lytham in July and to do that I've been advised not to play for a month.
Clarke has also had to pull out of the June 6-9 Nordea Masters in Stockholm.
He was first troubled by his groin during last month's Houston Open and it was again a problem in the PGA Championship at Wentworth.
Clarke missed the halfway cut on Friday at the European Tour's flagship event.
"I haven't been able to get through the ball properly and I don't want to take any chances," he added.
The US Open starts on June 14.