Mr Clapper said intelligence previously pointed out political grievances that threatened Egypt's regime.In testimony to Congress, Mr Clapper also warned of al-Qaeda's shifting threat to US security.
He also said the threat of cyber warfare was increasing and its impact was difficult to overstate.
The comments came a day after US Homeland Security chief Janet Napolitano said the threat of terrorism in the US was in some aspects at its highest level since 9/11.
'Long-lasting impact'
Testifying on Thursday before the House Permanent Select Committee on Intelligence, Mr Clapper said US intelligence services had done "yeoman's work" on Egypt.
They had pointed out political and economic grievances "for decades" that threatened President Hosni Mubarak's rule.
He added that popular unrest in the country would have a "long-lasting impact" on North Africa and the Middle East.
Mr Clapper said co-operation between intelligence services had helped to avert potentially deadly attacks in the US during the past year, including package bombs sent on two US-bound cargo planes.
But he added that al-Qaeda's core in Pakistan "continues to aspire to spectacular attacks", while militant groups in Yemen and Somalia were growing stronger.
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