Club England's operating costs - including the salaries of the England manager and his coaching team - decreased from £8million in 2011 to £6million last year, a saving of £2million over a period of around six months.
Capello quit in February last year after John Terry was stripped of the England captaincy, and agreed a severance package to cover the months before his contract - believed to be for £6million a year - was due to expire in July 2012.
The Italian was succeeded in May 2012 by Roy Hodgson, and the FA said Capello's salary and pay-off are confidential but confirmed that the costs related to Hodgson being England manager are less.
FA general secretary Alex Horne confirmed: "Roy earns less than Fabio did, but the deal with Fabio is confidential."
The accounts say: "Total expenditure remained consistent with 2011 at £21million with savings in the men's senior team coaching staff offset by increased tournament costs from the UEFA Euro 2012 finals."
The FA's overall revenue dropped slightly compared to 2011, £318m compared to £329m, caused by Wembley Stadium having hosted the Champions League final the previous season - earning the FA £3.6m.
The Olympic football tournament in 2012 also reduced the number of lucrative summer concerts the stadium could hold - for example in 2011 there were eight Take That concerts during the summer. It has also emerged that the FA may face a fight with Wales to host the final and semi-finals of Euro 2020.
Wales has joined England as among seven countries to have declared an interest in bidding to host the climax of the tournament but Horne admitted Turkish city Istanbul is the front-runner.
The other countries to have declared an interest are Germany, Spain, Belgium and Ukraine - all bar Ukraine and Turkey have also declared an interest in hosting group matches in the tournament, which is being played in 13 different cities across Europe, if they are unsuccessful in landing the final.
Horne said Istanbul was now favourite after losing its bid for the 2020 Olympics but that hosting group matches too would be important - it would guarantee England two home group games if they qualified.
Horne said: "There are several countries bidding for the final, and from our soundings you do sense there is a sympathy for Turkey with Istanbul having not got the Olympics.
"They are the front-runners but the prize of group games and a quarter-final or knockout match would be significant. It would mean two home games for England in the group, though we would still have to qualify."
Scotland and the Republic of Ireland have also declared an interest in hosting group games - indeed 32 of UEFA's 54 member nations have done so with a decision due in September next year.
- Sports & Recreation
- Roy Hodgson
- Alex Horne