Former Hearts attacker Skacel joined United in October on a short-term deal which is due to expire at the end of January.
Houston would like to keep the 33-year-old for the rest of the season, but is uncertain whether the club are prepared to hand the Czech the longer-term contract he is seeking.
"I have spoken to Rudi and what he wants is a longer-term deal," said Houston.
"He is 33. Given the age he is, he is looking to make a few quid from his next contract.
"If Rudi wanted to stay to the end of the season then I don't think that would be a problem. But if he wanted it for longer I would need to discuss that with the chairman to see what money is available.
"Rudi has his people working for him just now and you can understand why he would look at his options."