Appleton was reportedly in told in May that he would have in the region of £4m to spend on restructuring his playing squad before the transfer window closes.
However, he has since been informed that he will now only have around £1.5m available.
"It's slightly unprofessional," Appleton told BBC Radio Solent. "I'm not pleased about it but what can I do about it? I can't do anything about it but get on with it.
"I have been recruiting all summer, working on the basis that the budget was a certain amount. What you do is get the best 20 players you feel can fit that budget.
"If the budget is what is being reported at the minute then it makes the job very, very difficult. Those players I've recruited, a lot of them I won't be able to sign because we won't be able to afford them."
Pompey take on Plymouth Argyle in the League Cup tomorrow night.