Mr Clifton had been acting head of the department since the Spring. He will be responsible for BBC News Online as well as Ceefax, digital text, interactive TV and on-demand broadband services.
"As well as strong journalistic credentials, Pete will bring great creative leadership, together with knowledge and enthusiasm to the role," said Helen Boaden, director of BBC News.
He replaces Richard Deverell who left the role in July to become chief operating officer for CBBC.
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