In an interview with an Ecuadorean radio station the 25-year-old was quoted as saying West Ham had "forgotten" about him and were refusing to let him see another doctor.
But he has now retracted the comments with a statement on the club's website (www.whufc.co.uk).
"I have had a number of consultation meetings with specialists in London, accompanied by members of the club’s medical staff, and they have always kept me updated me on my injury," he said.
"It has been a frustrating time, but I would like to make clear that I have the utmost respect and confidence in the club’s medical team and the specialists I was referred to and I would like to apologise to them and the club for any issues arising from the recent press coverage.
"I will continue to work as hard as I can with them to return to help the team as quickly as possible, and continue the good start I made to the season."
Valencia injured a knee in the Europa League game at home to Astra Giurgiu last month and has not played since.
The club said last week that he would not be back in full training until the end of October.
With Andy Carroll and Mauro Zarate also out of action, the Hammers are short of attacking players ahead of Saturday's visit to Liverpool, where they have not won since 1963.
(Reporting by Steve Tongue; Editing by Ken Ferris)
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