The vote was organised by personal finance website Moneysavingexpert.com, which aims to donate at least £100,000 a year to charity.
Martin Lewis, founder of the site, said suspicious voting patterns were noticed and monitored but did not affect the result.
"We don't think it affected the top four," he said.
More than 36,000 votes were cast. The winners were: Help for Heroes, the charity for injured military personnel, with 7,770 votes; overseas aid charity Shelterbox, with 6,511; debt adviser Cap UK, with 4,146; and Samaritans, with 3,898.