Twelve posts entitled "Hacked by the Syrian Electronic Army" appeared on the FT's affected feeds, including its FT Markets account and The Lex Column, following a phishing attack on the company's email accounts.
A spokesperson for one of the world's leading business newspapers confirmed the hack and said the organisation was "working to resolve" the problems "as quickly as possible".
"We have now locked those accounts and are grateful for Twitter's help on this," Robert Shrimsley, the managing editor of FT.Com, said on the newspaper's website.
The SEA, who first emerged in 2011, are anonymous supporters of Bashar al-Assad and believe that media coverage of the Syrian civil war from Arab and Western countries is heavily biased.
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In an email interview with the FT a month ago, the SEA had promised to "target all the countries who support the terrorists groups in Syria".
Their most successful hack to date involved tweeting from the AP news agency's account that US President Barack Obama had been injured in a bomb blast at the White House.
A recent hacking of the UK's 'Guardian' newspaper, also thought to be executed by supporters of Assad's regime in Syria, took the form of emails to journalists, apparently from colleagues and containing plausible links to 'Guardian' news articles.
The SEA believe they are waging a cyber war and have also targeted media organisations such as the BBC and al-Jazeera.