He is the highest-ranking US official to publicly implicate Beijing since news of the data breach emerged.
China always dismissed suggestions that it was behind the hacking.
The statement comes after three days of high-level talks in which China and the US agreed to a "code of conduct".
"China remains the leading suspects," said Mr Clapper at a conference in Washington DC, but "the US government continues to investigate" he added, according to his office.
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At the Washington talks where cyber security was a top priority, US Secretary of State John Kerry said there was a need to work with China to develop a "code of conduct" on state behaviour in cyberspace - Chinese representatives had agreed with these conclusions.
"It's something that we agreed needs to be addressed and hopefully it can be addressed soon," State Department spokesman John Kirby said on Thursday.
China has said any suggestion that it was behind the hacking is "irresponsible and unscientific".

A car bomb exploded by the hotel in Bulo-burde where African Union (AU) and Somali officers were staying and gunfire continued for another five hours, witnesses said.
Six soldiers were killed, including a top Somali army commander, the AU said.
The al-Shabab Islamist group said it was behind the attack and that 30 AU and army officers had been killed.
A spokesman for the 22,000-strong AU force in Somalia (Amisom), Col Ali Adan Humad, said all the al-Shabab fighters involved in the raid had been killed, without specifying numbers.
Al-Shabab, which is linked to al-Qaeda, has waged an eight-year insurgency to overthrow the weak UN-backed government and create an Islamic state in Somalia.
The BBC's Ibrahim Ade in the capital, Mogadishu, says al-Shabab had occupied Bulo-burde for more than five years.
The town, which has a strategic bridge over the River Shabelle and is at a crossroads linking various regions of the country, was an important base for al-Shabab.
Bulo-burde was captured as part of an ongoing AU and government offensive against al-Shabab, which controls much of south and central Somalia.
Communications to the central Hiran region went down not long after the fighting and gunfire in Bulo-burde ended, our reporter says.
Witnesses told the BBC the car blast at the hotel happened at 02:00 local time (23:00 GMT) and the fighting went on until about 07:00.
Col Humad said three Djiboutian soldiers and three Somali soldiers, including Col Mohamud Amin - the military commander of Hiran who was leading the offensive in the region - were killed.
Ten soldiers were also wounded, he said.
Earlier, Col Humad denied there were casualties when an Amisom convoy was attacked near its base in Arbiska outside Mogadishu.
Al-Shabab had released a statement saying that seven Burundian peacekeepers and five American nationals travelling in the vehicles were killed on Monday afternoon.
The al-Qaeda-linked group lost control of Mogadishu in 2011, but has intensified bombings and mortar raids in the city in recent weeks.
Last month, al-Shabab fighters stormed Villa Somalia, the seat of government in Mogadishu, killing at least 11 people.
China is the "leading suspect" in the massive hack of a US government agency holding the personnel records of millions of Americans, US intelligence chief James Clapper has said.
[NEXT_CONCEPT]
Somali Islamist fighters have attacked a hotel in a strategic central town the militants lost control of last week.