The row centres on Emap's intention to shut down its Freeview music channel, The Hits, and replace it with the 4Music format, a joint-venture online music video service that Emap and Channel 4 want to transfer to TV.
Sources said that the plan is to launch 4Music on Freeview and other digital platforms from January, with Channel 4 sales taking on airtime sales for the channel.
Sky is thought to object to this, as it has a four-year contract, running until 2009, which gives it rights to sell airtime across all of Emap's music TV stations. If the move goes ahead, it could result in a significant loss of revenue.
Sky is said to be in talks with its lawyers over potential breach of contract and what action, if any, it can take if Emap closes The Hits.
A report in the Financial Times this week stated that Emap is in talks with Channel 4 over a sale of its TV assets, which include brands such as The Box and Kerrang! as well as The Hits. It is unclear how any sale would affect Emap's airtime deal with Sky.
Sky refused to comment. An Emap spokeswoman said: "It is business as usual with Sky."