The former US ambassador to the Philippines arrived late on Tuesday and had already met Philippine President Gloria Arroyo, embassy spokesman Matt Lussenhop said on Wednesday.
Negroponte was also due to meet other top security officials on intelligence matters and the threat.
Philippines presidential spokesman Ignacio Bunye said Arroyo had dinner with Negroponte on Tuesday, but refused to say what the two discussed.
Negroponte's visit is not believed to be linked to the threat that prompted the US embassy to close on Tuesday.
It remained shut on Wednesday, and the embassy was still evaluating when it could reopen, spokesman Lussenhop said.
During his visit, Negroponte, 65, who heads 15 US intelligence agencies, will discuss "the full gamut of [security] issues but obviously terrorism is the highest on the list", Lussenhop added.
A threat prompted the closure of
the US embassy on Tuesday
The Philippines has been a key ally of the United States in the "war on terror", even while battling local Muslims with links to al-Qaida and Jemaah Islamiyah.
The nature of the threat to the embassy has not been disclosed, but Philippine police have dispatched bomb squads to search the area.
Security has also been tightened around other embassies in the country.
Earlier this year, Philippine authorities said they had thwarted a plot by Jemaah Islamiyah and their local allies to mount a 1000-kg truck bomb attack on the US embassy.
The embassies of Australia and Britain, also key US allies in the "war on terror", were also eyed as targets, officials said.