The report on weapons of mass destruction was put together by a team of 15 FT journalists and production staff.
The major three-part investigation revealed the spread of nuclear, chemical and biological weapons in 35 key countries around the world, exposing who has what, suspected research programmes, missing stockpiles and striking ranges.
Other winners included Best Overall Journalism Service, which was won by , the news and current affairs portal for the Barcelona region.
Transitions Online, the Prague-based online news magazine that covers the post-communist region of Eastern and Central Europe, the Balkans and the former Soviet Union, won the Best Innovation in Online Journalism category.
The Best Use of Multimedia award went to two journalism students from the Danish School of Journalism, the first time student journalists have won any of the prizes.
Dr David Whitehouse, the BBC's science correspondent, won the Best News Story Broken on the Net category and has now won awards for four years running, and the Outstanding Contribution to Online Journalism in Europe award went to Mike Smartt, editor-in-chief of BBC News Interactive.
The awards were launched in 1999 and this year more than 1,000 entries were put forward from across Europe. The competition was judged by 118 representatives from European media organisations and journalism schools.
Tracy Corrigan, editor of FT.com, said: "This award proves again that FT.com is an invaluable site for in-depth news and analysis. The special weapons of mass destruction report is journalism at its best, and an outstanding achievement for the team involved."
Since its relaunch in May 2002 as a subscription website, FT.com has attracted 3.5m unique monthly visitors, generating more than 55m page views.
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