Sepp Blatter is eager to rebuild bridges between FIFA and Brazil ahead of the 2014 World Cup and has requested a meeting with the country's president.
The troubled partnership hit an all-time low at the weekend following criticism of delays by FIFA secretary general Jerome Valcke, with the Brazilian government responding by saying they no longer wanted to deal with him.
A written apology from Valcke came on Tuesday, followed by Blatter's efforts to make contact with Brazil's sports minister Aldo Rebelo.
But Blatter's letter makes it clear that time is running out for both sides to put their troubles behind them.
Blatter's letter states: "Please allow me to express my deepest regret for the present situation. I am gravely concerned about the deterioration in the relationship between FIFA and the Brazilian government, a relationship that has always been characterised by mutual respect.
"You have also received a letter from the FIFA secretary general Jerome Valcke and I have no further comment on this matter other than to say that both as FIFA president and personally, I would like to apologise to all those - above all the Brazilian government and President Dilma Rousseff - who feel that their honour and pride has been injured."
The letter adds: "Brazil deserves to host the World Cup and the entire world is looking forward to it. However, the sands of time have been running since 2007.
"Therefore, let us not waste time on entrenching our positions. Let us instead build something great together, as promised by President Lula during his presidency. I will be travelling in Asia in India, Bangladesh, Bhutan and Nepal until 10 March, and afterwards I would like to meet President Rousseff and yourself as soon as possible - ideally next week."