FIFA president Sepp Blatter apologised for remarks by one of his top executives about Brazil's preparations for the 2014 World Cup.
Blatter's comments came in a letter to the government Monday, a day after secretary general Jerome Valcke sent his own apology.
The government informed FIFA it would no longer deal with Valcke after he said: "You have to push yourself, kick your arse" to speed preparations. It remained unclear whether the government would accept the apologies and change its position regarding Valcke.
The government says Sports Minister Aldo Rebelo would first answer the letters from FIFA before making his decision public.
In a letter released by the sports ministry, in Portuguese, Blatter expressed his "deepest regret" about the situation.
"I'm extremely worried about the deterioration of the relationship between FIFA and the Brazilian government," he said. "My only comment regarding this subject is to apologize to everyone who may have had their honor and their pride hurt, especially the Brazilian government and President Dilma Rousseff."
Blatter said Brazil and FIFA have a "goal in common" and must work together to organize an "extraordinary World Cup in the country of football, in the country of champions."
But he warned that "time is passing by" since the country was picked to host soccer's showcase event in 2007.
"We shouldn't let conflicts make us lose time," he said.
Blatter, who is in Bangladesh to discuss soccer with national federation officials, said he hopes to meet with Rousseff next week in Brazil.
