Fifa president Sepp Blatter still intends to travel to Canada for the final of the Women's World Cup this month despite the crisis engulfing world football's governing body.
General secretary Jerome Valcke announced on Monday that he will not be making the trip.
He was due to attend the opening of the tournament, which begins on 6 June.
"It is important that he attends to matters at Fifa's headquarters in Zurich," read a statement.
BBC Radio 5 live sports news correspondent Richard Conway called Valcke's decision a "highly unusual move".
Fifa in crisis
Fifa has been dogged by corruption allegations but became embroiled in fresh controversy last week when seven officials were arrested on charges of racketeering, wire fraud and money laundering.
The arrests - a result of a United States prosecution - took place in Zurich last Wednesday as Fifa officials from around the globe gathered in the Swiss city for their latest congress.
On the same day, Fifa was also rocked by the news that Swiss authorities had begun a separate criminal investigation into how the 2018 and 2022 World Cups were allocated.
Blatter was encouraged to quit in the wake of the arrests but was re-elected as Fifa president for a fifth term of office on Friday, claiming he was the man to lead reform of the organisation.
Fifa has provisionally suspended Concacaf general secretary Enrique Sanz from all football-related activities.
The Colombian was banned following investigations carried out by Fifa's ethics committee and the latest facts presented by the US Attorney's Office for the Eastern District of New York.
Concacaf, which has its headquarters in Miami, governs the game in North and Central America as well as the Caribbean.
Congolese Football Association vice-president Jean Guy Blaise Mayolas and general secretary Badji Mombo Wantete have also been suspended for apparent "breaches of the Fifa code of ethics".
Brazilian authorities are investigating Ricardo Teixeira, the former head of their national football federation, for alleged money laundering and fraud.
Teixeira's successor as president, José Maria Marin, was one of seven Fifa officials arrested by Swiss police on charges of corruption.
A judge in Paraguay has also ordered the arrest of Nicolas Leoz, the former head of the South American Football Confederation.
Leoz is wanted by US authorities and will be put under house arrest.