The Asian zone preliminary round second-leg tie will be one of the first important international sporting events to be held in Pakistan since gunmen attacked the Sri Lankan cricket team bus in Lahore in 2009, killing seven people.
"We have been in contact with the Asian Football Confederation (AFC) and neither organisation has so far received any communication or request related to this two-legged qualifying match, contrary to recent media reports," FIFA told Reuters in an email.
"Prior to the qualifying competition kicking off, FIFA, in conjunction with its confederations sought to establish any countries where matches could not currently take place, either due to more long-term internal problems, or more recent events such as in Syria and Yemen.
"However, Pakistan was not on that list."
FIFA added that Pakistan had already hosted an Olympic Games qualifier against Malaysia in March at the Punjab stadium, Lahore, where the July 3 match is due to be held.
Bangladesh football federation president Kazi Salahuddin said on Monday that FIFA had turned down its request to relocate the match.
"During the FIFA congress in Zurich earlier this month we requested them to allow us to play both legs in Dhaka. But they did not agree," Salahuddin told reporters.
Bangladesh said former coach Robert Rubcic, fired on Tuesday after a pay row, had been reluctant to travel to Pakistan.
Six Pakistani policemen and a driver were killed in the attack in March 2009 while five Sri Lankan players were also wounded in the team bus which came under attack near the Gaddafi stadium.
Afghanistan last month became the first foreign cricket team to play in Pakistan since the attack when they played a Pakistan A team.
Neither Pakistan nor Bangladesh have ever qualified for a football World Cup and neither team is seen as having a realistic chance of playing in Brazil in 2014.
The first leg of the tie will be in Dhaka on June 29.
