Two Vietnamese tourists killed earlier on Friday and ten others were injured in a tourist bus explosion in Marioteya district, near Giza governorate.
The ministry confirmed that two Vietnamese tourists were killed when a roadside bomb went off, while the state prosecutor's office said a third tourist died later.
According to officials, the explosion occurred at 6:15PM local time when the bus passed a section of wall used to hide the device from motorists and pedestrians. No militant group immediately claimed responsibility for the attack.
"The DFA today advised Filipinos planning to travel to Egypt to exercise a higher level of vigilance when visiting tourist destinations there", the agency said in a statement.
The bus was carrying a total of 16 people including 14 Vietnamese tourists, an Egyptian driver and a tour guide, according to the statement.
Without advising authorities, the bus deviated from the route established by the interior ministry for vehicles bringing visitors to Giza, Madbuli said.
Two of the injured are in critical condition.
Egypt has for years been battling an insurgency in North Sinai, which surged following the 2013 military ouster of president Mohamed Morsi.
The government says fighting Islamist militants is a priority as it works to restore stability after the years of turmoil that followed the "Arab Spring" protests of 2011.
Friday's attack however is the first attack to target foreign tourists in nearly two years.