Shrimpers chairman Ron Martin last week revealed that the influential 27-year-old had turned down the opportunity to discuss a new deal at Roots Hall.
However the ex-Everton and Blackpool man, whose contract expires in the summer, has dismissed these claims outright and insists he could still be with the club next season.
"I've never asked to leave Southend and I've certainly not ruled out staying," Clarke told the Southend Echo.
"I saw what the chairman said about the situation and it was quite surprising and disappointing too if I'm honest.
"I thought we were going to sit down after our final two games and go from there but I don't know whether that's changed now."