"This act of terrorism... will have wide effects on our economy, trade, tourism and image in the eyes of the world."
The attacks, with homemade bombs, were on the basement car park of the Marriott and a restaurant in the Ritz-Carlton, police said.
Police said that two suicide bombers were involved, and at least one attacker, and possibly more, was staying at the Marriott.
An unexploded bomb and other explosives material were found in room 1808, which officials said was the "control centre" of the attacks.
National police spokesman Nanan Soekarna said: "We still don't know who booked room 1808."
Gen Wahyono said a suicide bomber was suspected of carrying out the car park attack as a severed head was found there.
AT THE SCENE
Karishma Vaswani, BBC News, Jakarta
It was a scene of confusion and chaos outside the Ritz Carlton and JW Marriott hotels this morning. Ambulances and security forces arriving at the hotels came to rescue the injured and treat anyone who was hurt.
People milled around outside, onlookers wondering what had happened as hotel staff and guests stood around shocked on the streets. The blasts took place at breakfast time in one of the most prestigious areas in Jakarta's commercial centre.
Many Indonesians we spoke to this morning told us how shocked and upset they were by what had happened here today and how worried they are about the damage this will do to the reputation of their country.
New Zealand's Prime Minister John Key confirmed a New Zealand national was among the dead.
Reuters news agency named him as Tim Mackay, president director of PT Holcim Indonesia, quoting the company's marketing director Patrick Walser.
Australian Prime Minister Kevin Rudd condemned the attacks as "barbaric".
He said he had "grave concerns" for an embassy official and two other missing Australians.
US Secretary of State Hillary Clinton said they were "senseless" and that the threat of terrorism remained "very real".
The Manchester United football team was due to arrive in Indonesia on Saturday and was booked to stay at the Ritz-Carlton.
The team have now called off the Indonesian leg of their tour, saying they "cannot fulfil the fixture in Jakarta" against an Indonesia Super League XI on 20 July.
The two blasts, in Jakarta's central business district, occurred at about 0730 (0030 GMT).
Dec 2000 - Church bombings kill 19
Oct 2002 - Bali attacks kill 202, many Australian
Dec 2002 - Sulawesi McDonalds blast kills three
Aug 2003 - Jakarta Marriott Hotel bomb kills 12
Sept 2004 - Bomb outside Australian embassy in Jakarta
Sept 2005: Suicide attacks in Bali leave 23 dead, including bombers