Gatland admitted he is left in a quandary and will have to assess the situation after Sunday's opening World Cup clash against defending champions South Africa in Wellington.
"The thing is if we do replace him and if he does recover in two weeks and we pick up another injury, you can't recall that player."
Jones missed selection in the Welsh squad for the 2003 World Cup and withdrew from the 2007 tournament with a shoulder injury.
"We just want to see how Sunday goes and hopefully we won't pick up any injuries and we've just got to give (Jones's') injury a little bit more time to settle," Gatland added.
"It's a long tournament and we've got to make sure we make the right decision there. Obviously, if we pick up injuries on Sunday that's going to change our thinking, so we have to see what happens."
Jones won selection in Wales' 30-man World Cup squad after convincing team medical staff of his fitness after playing only 30 minutes in three warm-up matches, missing wins in Cardiff over England and Argentina.
On the Welsh squad's arrival in New Zealand he had been confident of breaking his World Cup jinx.
"There is always the moment where you think 'oh no, not again'," Jones said. "You never know what will happen.
Playing at the World Cup is always something I have dreamed of doing and now I am really looking forward to it.
"The fact I have never been to a World Cup before means I have nothing to compare this to. But I want to experience one. I want to do my best for my team and my country," he added.
Gatland said prop Gethin Jenkins and flyhalf Stephen Jones, who were not considered for the South Africa match because of injuries, were expected to return to full training from next week.