The club's general manager, Christine Wright, said reports the SFA is considering relocating its offices from the National Stadium were a "surprise".
But she added that the two groups have a good relationship and would work together to resolve the situation.
Ms Wright said: "As any large scale business would do when there is an important event such as the renewing of a lease coming up, theSFA are looking at various options.
"One of these options is leaving Hampden and it would have been strange if it had not been in the mix.
"However as far as we are concerned it is business as usual."
The SFA is 14 years into a 20-year lease at the National Stadium, which is owned by Queen's Park.
The association is discussing proposals, including committing for a further 20 years, buying Hampden outright from the amateur side or moving from the South Side complex.
Any move would see Scotland games being played at either Celtic Park and Ibrox Stadium in Glasgow, Aberdeen's Pittodrie Stadium, Hibernian's Easter Road ground or Murrayfield stadium in Edinburgh, the home of Scottish rugby.
However, SFA Chief Executive Stewart Regan has dropped a strong hint Hampden will continue as the home of Scottish football, but said the SFA would keep its options open.
A consultancy firm has been employed by the SFA to consider future options.
A briefing note to the SFA and Hampden Park Limited suggested one alternative was to move Scotland games and the two major cup finals away from Hampden.
The SFA and SPFL offices, and the Scottish Football Museum, would also be relocated in that event.
Mr Regan said: "I must stress that this process is at a very early stage, and it is hugely misleading to suggest that the Scottish FA is focusing on whether to move away from Hampden Park.
"Given its historical importance, Hampden remains a key pillar of the national game."
The SFA still with five-and-half-years left of its current rental agreement and will make a decision on renewing some time after the Euro 2020 vote.