Siniora said there are no warships in Lebanese territorial waters, except Lebanon's small navy - made up of patrol boats - and the 12 warships belonging to a UN peacekeeping force.
According to Gordon Johndroe, a White House spokesman, Washington has had "regular consultations" with Siniora and other US allies in the region.
"There's constant communications at various levels," he said.
The US declined to say whether the decision to deploy the USS Cole was a show of force aimed at Syria, which it has accused of interfering in Lebanon.
Lebanon's governing coalition and the Hezbollah-led opposition have failed to reach a deal over the election of a new president.
A senior US official said Washington was "very concerned" about the situation in Lebanon and called the move "support for regional stability".
"The United States believes a show of support is important for regional stability." the official.
Nabih Berri, the parliament speaker, who is aligned with the opposition, has linked the deployment of the warships to Israel's raids in Gaza Strip.
"The target [of US warships] is Gaza. It is aimed to allow what must happen in Gaza to happen without anyone moving to support [the Palestinians]," he said.
"This is a real threat, not merely a muscle-flexing."
Berri also said that the US military move was designed to focus attention on Lebanon "in order to cover up the massacres being committed in Gaza.
"This [US] fleet comes to back Israel so that it can complete its plan," he said
'Gun boat diplomacy'