Speaking to the Lords communications select committee, Thompson said that "increasingly, remuneration is a factor" in making top BBC jobs less attractive to applicants.
Thompson was speaking ahead of today's announcement that George Entwistle has been appointed director of BBC Vision, after fulfilling the role on an acting basis since the turn of the year.
The corporation ran an "extensive recruitment search" for the prestigious Vision post, but decided that BBC Knowledge controller Entwistle was the right person for the role.
Despite the healthy £300,000+ annual salary mooted for the ideal candidate to lead Vision, Thompson said that the BBC is struggling to compete for top talent in "broadcasting markets, which are commercial".
Previous BBC Vision director Jana Bennett received total remuneration of £517,000 during her final year in the post, before joining BBC Worldwide.
According to sources reported in The Guardian, the decision to cut the salary on offer was a dissuasive factor for some candidates. One insider said: "The fact the salary that was on offer - although that may have had to change - started with a three put off some people."
In 2009, the BBC bowed to public pressure by agreeing to cull more than 100 senior managers and also trim top executive pay by 25% by 2013. Thompson and other senior directors also agreed to waive bonus payments and work one month for free to help cut costs.