"A stress fracture has been revealed on his left ankle which requires six to seven weeks rest, so he is out of the Sri Lankan tour," Pakistan Cricket Board director of operations Salim Altaf told AFP on Tuesday.
The 30-year-old fast bowler took 17 wickets in Pakistan's 2-0 Test series win over England in December but the injury flared up during the recently-ended Test series against India.
He was forced to miss the first two One-day matches against India before being ruled of the rest of the limited overs internationals on Sunday.
"Akhtar's injury is a blow to Pakistan because he has been our main strike bowler. But hopefully this will give some youngsters a chance to fill the gap," said chief selector Wasim Bari.
Pakistan play two Tests and three One-day matches on their tour of Sri Lanka.
"Akhtar will resume training after six weeks' rest. Only after that will we assess his chances of touring England, which is an important series," said Bari.
Pakistan are scheduled to play four Tests and five One-day matches on their tour of England starting from early July this year.