The Robert Koch Institute, responsible for disease control and prevention, said a 22-year-old woman was in hospital in Hamburg and that a 37-year-old woman and a man in his late thirties were in separate hospitals in Bavaria.
All three recently returned from Mexico, officials said.
Spain and the UK earlier confirmed two cases each and six other EU states have been monitoring patients suspected of having the virus.
At 64, the US has the greatest number of confirmed cases outside Mexico. The state of California has declared a state of emergency and President Barack Obama is asking Congress for an additional $1.5bn dollars to bolster the US response.
A US federal health official, Dr Richard Besser of the Centers for Disease Control and Prevention, said on Tuesday: "As we continue to investigate cases here, I expect that we will see deaths in this country."
Canada, New Zealand and Israel have also detected the virus, and other states with suspected cases include Australia, South Korea and Peru.
In Mexico, there is some confusion over exactly how many people died from H1N1, the BBC's Stephen Gibbs reports.
From Matthew Price in Oaxaca, Mexico
The first fatal case of the virus is believed to have been contracted here in Oaxaca. It is a tourist centre and the obvious concern is that when the visitors leave, they may take the virus with them.
At the local cemetery, a group of gravediggers pointed me towards a freshly dug plot. The flowers on top had wilted under the sun but still had some colour. Here was the grave of the first confirmed victim of the virus, Adela Gutierrez, 39.
One of the gravediggers, Sergio Castro Lopez, told me people here are worried. They are waiting for the authorities to tell them what they should do. I tried at the local hospital to get more information but the ministry of health has ordered its staff across the country to remain silent.
This is largely because the government is now subjecting the samples it has from deceased patients to a more laborious verification process.
Meanwhile, the search for the source of the outbreak continues, with the focus on the vicinity of a pig farm in the eastern part of the country.
The Mexican government is urging against jumping to conclusions and is suggesting the possibility remains that the virus originated outside the country, our correspondent adds.
The capital, Mexico City, has banned restaurants and cafes from serving all food except takeaways to try to prevent the spread of the virus.
Schools across the country have closed, public gatherings are restricted and archaeological sites have been placed off-limits.
California governor Schwarzenegger: 'We are taking strong and swift action'
Mexico City's chamber of trade estimated restrictions in the city were costing businesses there at least 777 million pesos ($57m or £39m) a day.
People have been cancelling beautician appointments, wary of close physical contact, Reuters news agency reports.
"The customers are scared stupid - they don't want to go out," said hairdresser Esther Gonzalez.
The World Health Organisation has called a meeting of scientific experts for Wednesday to discuss the situation and the exact nature of the outbreak.
SYMPTOMS - WHAT TO DO
Swine flu symptoms are similar to those produced by ordinary seasonal flu - fever, cough, sore throat, body aches, chills and fatigue
If you have flu symptoms and recently visited affected areas of Mexico, you should seek medical advice
If you suspect you are infected, you should stay at home and take advice by telephone initially, in order to minimise the risk of infection
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