Blatter will travel to Brasilia to try to patch up the differences after FIFA secretary general Jerome Valcke infuriated the Brazilians by saying organisers needed "a kick up the backside" over slow preparations for the tournament.
"The meeting, which will also be attended by Brazil sports minister Aldo Rebelo, has been confirmed by the two entities today," FIFA said in a statement.
Valcke's remarks caused uproar in Brazil, prompting the government to notify FIFA it would no longer accept the Frenchman as the governing body's point man for the World Cup.
Blatter sent a letter offering an "apology to all those who had their honour and pride wounded, especially the Brazilian government and President Dilma Rousseff."
Rebelo accepted the apology but declined to say if Brazil would reconsider and agree to work with Valcke again.
Valcke has been forced to postpone a tour of construction sites in World Cup host cities until after the meeting which is likely to decide his role.
Brazil is struggling to prepare for the World Cup and its curtain-raiser, the 2013 Confederations Cup.
Stadium construction was slow to get started, costs have ballooned and vital infrastructure projects such as hotels, roads and airports are way behind schedule.
Rousseff has made improving infrastructure in time for the World Cup one of the main priorities of her government.
Valcke was widely credited with the success of the 2010 World Cup in South Africa, overseeing the preparations and cajoling local organisers into action when they threatened to fall behind schedule.
However, he has not been able to exert the same influence in Brazil and has become exasperated at the country's Congress over its delays in approving a so-called World Cup bill.
This would bring in temporary legislation which would overturn a ban on the sale of alcohol in Brazilian stadiums and may rule out discounted tickets for students, pensioners and native Indians.
Brazil's preparations suffered a further setback on Monday when Ricardo Teixeira, the head of the Brazilian Football Confederation and local organising committee, resigned.
Teixeira blamed health problems although his decision came following a string of corruption allegations. Sports minister Orlando Silva also quit in October over corruption allegations.
Brazil, record five-times world champions, last hosted the World Cup in 1950.