Philippines Trade Minister Ramon Lopez told CNN the country "would not stop trade and investment with the US."
"(Duterte) has decided to strengthen further and rekindle the ties with China and the ASEAN region," Lopez said, referring to the Association of Southeast Asian Nations.
"America has lost now. I've realigned myself in your ideological flow," President Duterte told business leaders in Beijing on Thursday.
"And maybe I will also go to Russia to talk to Putin and tell him that there are three of us against the world: China, Philippines and Russia. It's the only way."
In a statement Friday, Duterte's office said the Philippines had no intention to renege on treaties or agreements with established allies.
The President's comments were "an assertion that we are an independent and sovereign nation, now finding common ground with friendly neighbors with shared aspirations in the spirit of mutual respect, support and cooperation," the statement said.
'Troubling rhetoric'
In a statement, the US Embassy in Manila blasted Duterte's comments as "creating unnecessary uncertainty."
"We've seen a lot of this sort of troubling rhetoric recently which is inexplicably at odds with the warm relationship that exists between the Filipino and American people and the record of important cooperation between our two governments," embassy spokeswoman Molly Koscina said.
The US will honor its alliance commitments and treaty obligations, and expects the Philippines to do the same, she added.
Beijing rejected a recent international court ruling in Manila's favor, and has long called for bilateral negotiations in which other parties do not participate.
In a statement, China's Ministry of Foreign Affairs praised Duterte's willingness to address "territorial and jurisdictional disputes by peaceful means ... through friendly consultations and negotiations by sovereign states directly concerned."
'Maybe he's joking'
In Manila, many greeted the news with shock.
"Maybe he's only joking," saleswoman Marisa Laguitan, 59, said.
"America is very friendly and a very long (term) friend of Filipinos."
Ian Duly, 34, said he had nothing against the US, but "it's about time for a change."
"I believe in Duterte," he added. "It's about standing up for your people."
Speaking to CNN Philippines, one call center worker worried about the effect the move could have on her industry.
"What if BPOs disappear in the Philippines? We won't have a job," she said, referring to business process outsourcing.
Duterte 'delusional'
Lopez, the trade minister, dismissed concerns that Duterte's shift would endanger the country's economy.
"What we are saying is that there will be less dependence just on one side of the world," he told CNN.
"As you know we have been strong partners with the US so its basically just trying to balance the partnership and also strengthening this side of the world, specifically with China."
He said Duterte was pursuing an independent and "more sovereign" foreign policy, adding that the US-Philippines relationship was strong and "cannot just be eliminated."
Duterte's opponents at home were damning however.
"(He) has a really inflated, if not delusional, view of himself as a strongman at the level of China and Russia's leadership," Senator Leila De Lima, a longtime critic of the President, said in a statement.
Former foreign minister Albert Del Rosario warned of cosying up to a country like China that doesn't share "our core values of democracy (and) respect for human rights."
"Casting aside a long time reliable ally to hastily embrace an aggressive neighbor that vehemently rejects international law is both unwise and incomprehensible," he said in a statement.
CNN's James Griffiths wrote and reported from Hong Kong, Matt Rivers reported from Beijing, Pamela Boykoff reported from Manila. CNN's Katie Hunt, Kathy Quiano, Nicole Gaouette and Elise Labott, and journalist Charie Villa all contributed reporting.