Published yesterday, the corporation's annual report revealed that its pay to on-screen talent fell £7.7m, or 3.3%, to £221.5m in the year ending March 31, 2010.
However, the BBC paid its top 15 senior executives a total of £4.76m last year, up from £4.6m in 2008/9. Total BBC pay also increased from £1,003bn to £1,012bn.
No bonuses were paid to any BBC executives apart from BBC Worldwide chief executive John Smith, who helped guide the commercial division to record profits of £145.2m last year, up 36% year-on-year.
The corporation has pledged to cut the pay of its over 600 executives by around 25% in real terms by 2013, with all the BBC directors due to work for one month without pay in the next two years.
Speaking at a press conference yesterday, Thompson said that the increase in senior executive pay revealed in the annual report does not fully reflect the salary freezes and bonus cuts brought in by the BBC last August.
"We've made tangible progress. We expect BBC director pay to come down absolutely in line with executive pay as a whole," said Thompson, who took home £838,000 last year, up from £834,000 in 2008/09.
"Even if you compare the BBC with the private sector or public sector, it was a tight settlement."
BBC Trust chairman Sir Michael Lyons added: "I do absolutely understand the difficulties looking at something that's now the best part of six months old.
"You've got to take these [figures] and then make a judgment…is the BBC further tightening up the remuneration?"
The BBC also yesterday published the results of a study into public perceptions of its pay to top talent and senior executives.
The report found that the BBC's contract with Jonathan Ross "tended to be the focal point of most discussion", but executive salaries and expenses actually seemed to "inflame passions even more than talent costs".
The BBC has agreed to publish the pay of its top stars in salary bands, along with releasing the names of its highest earners, such as Jeremy Clarkson and Graham Norton.
However, it will not reveal exact details about individual contracts as BBC director general Mark Thompson believes that would be "damaging and destructive".
Speaking about the study, Lyons told The Guardian: "The research we've published shows that the public don't want to see salaries attached to an individual.
"Whilst people were concerned about top talent pay they wouldn't go as far as naming individual salaries. We've no intention of doing that so that's not a problem."
Lyons also discussed the decision to reprieve digital station BBC 6 Music, which was facing the axe under Thompson's strategy review.
He said that there was an unsurprisingly strong public response to the station's proposed closure, which helped persuade the Trust to reject the plan.
Lyons has now called on the BBC Executive to produce a "proper and coherent strategy" for digital radio. However, he added: "We're not saying then we'll even reach a different decision [about 6 Music]. It's on hold. We're not convinced."