The raid intensified pressure on Munich-based Wirecard, a constituent of Germany's blue-chip DAX index that has shed $10 billion in value since the FT ran the first of a series of three investigative reports at the end of January.
Wirecard has rejected the FT reports as defamatory and said earlier on Friday it would sue the newspaper.
"Police confirm that they have raided the premises of Wirecard entities in Singapore," a police spokeswoman told Reuters.
Singapore police opened inquiries this week following the FT's reporting, which cited the preliminary findings of an investigation by law firm Rajah & Tann that found evidence of series offences of forgery and false accounting.
Wirecard said: "We actively approached the authorities yesterday and pledged our full cooperation in the investigation activities.
"This morning, Wirecard met with Singapore law enforcement at Wirecard's headquarter in Singapore and provided the police with comprehensive supporting material in regards to their enquiry into the defamatory allegations in the FT series of articles.
"We would like to reconfirm that the accusations against employees of Wirecard are unfounded. We are working closely with the Singapore police to clear all allegations."
The FT did not respond to a request for comment.
Wirecard CEO Markus Braun, the company's largest shareholder with a 7 percent stake, said on Monday that no evidence had been found of criminal misconduct either by the company's own compliance team or by Rajah & Tann. Investigations were continuing and would be finished quickly, he said.
Wirecard, founded in 1999, has been a perennial target for speculative short sellers - market players who seek to profit from falls in a company's share price - who have questioned its accounting methods and rapid international expansion.
Yet it also has strong support in the financial community, with 24 out of 28 market analysts rating the stock either a 'strong buy' or a 'buy', according to Refinitiv data.
Their median price target is 210 euros - more than double Friday's level of 101.15 euros, down 9 percent on the session.
An FT story, published online on Thursday, alleged that Wirecard staffers had engaged in the 'round tripping' of funds to inflate reported revenues, and that managers from its Munich head office had been aware of the practice.
"In the article published yesterday, Wirecard employees are slanderously prejudged with unproven and false allegations," Wirecard said in an earlier statement.
"We will use all available legal means to protect the company and in particular our employees and their personal rights. Wirecard is taking legal actions against FT and its unethical reporting."
Wirecard did not say in which jurisdiction it planned to bring legal action. A spokeswoman added the company would act to protect the personal reputations of individuals named in the newspaper's reporting.
The company was also cooperating with the authorities in ongoing investigations into suspected market manipulation in Wirecard stock being conducted by the Munich state prosecutor with the backing of financial regulator Bafin.
Contacted by Reuters, the Munich prosecutor said it was aware of the Singapore police raid but this did not change its view that there was insufficient evidence to launch a criminal probe against Wirecard's managers.
(Reporting by Douglas Busvine, additional reporting by Rachel Armstrong in London; Editing by Keith Weir; Editing by Michelle Martin/Keith Weir)
By Douglas Busvine and John Geddie