"A lot of us have seen the pictures about what happened here and pictures don't do it justice," he said, standing in front of a bungalow without a roof.
The twister killed at least 11 people and wiped out an estimated 95% of Greensburg when it swept by on Friday.
Churches, the town hall, the hospital and nearly every dwelling has gone.
"There is a lot of destruction. Fortunately, a lot of folks had basements here in this part of the world and lived to see another day. Unfortunately, too many died," said the president.
He first saw the wreckage from his helicopter, and then did a short tour on foot.
Series of twisters
Greensburg was a town of about 1,500 people.
Residents who met the president said they were still shocked by the calamity that had befallen them.
"He was sorry about what had happened," said Kaye Hardinger.
"I would have invited him in for a cup of coffee, but I didn't have time to dust."
The tornado was the most damaging to hit the US in years but not the first big one this year. In March eight school pupils died when twisters barrelled through Alabama and Georgia, while another hit Florida in February.
Meanwhile forecasters are predicting a heavy hurricane season, with many large storms brewing in the Atlantic and the Gulf of Mexico.
The US response to natural disasters has been under scrutiny since Hurricane Katrina swamped New Orleans in 2005.
The head of the Federal Emergency Management Agency insisted that every assistance was offered to Kansas in quick time.
Kansas Governor Kathleen Sebelius originally said there was a shortage of national guard and mechanical help due to deployments in Iraq.
But that criticism appears to have died down, with local Mayor Lonnie McCollom saying he was more than satisfied with the federal response.
"From my perspective, all I can say is I have had all the help I have needed," he said.
Meanwhile, nearby towns were struggling with deep flooding brought on by the storm system, that dumped as much as eight inches (20cm) of rain in 24 hours on parts of Missouri, Iowa and Kansas.
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