"Rocket made it to drone spaceport ship, but landed hard. Close, but no cigar this time," Elon Musk, founder and chief executive of SpaceX, as the company is called, said on Twitter.
"Bodes well for the future," he added.
The Dragon cargo capsule itself was successfully launched into space and is expected to dock with the space station on Monday.
Seeking to cut the cost of space launches, SpaceX hoped to bring the rocket back to Earth, aiming to land it on a floating platform in the Atlantic Ocean some 200 miles (322 km) off Jacksonville, Fla., north of the Cape Canaveral Air Force Station launch site.
A ship stationed near the platform tried to capture the touchdown on video, but it was too dark and foggy, Musk said.
Engineers will look to work out what went wrong by studying data relayed during the descent, as well as pieces of the rocket itself, he added.
"Ship itself is fine. Some of the support equipment on the deck will need to be replaced," said Musk, who prior to the launch had put the odds of a successful touchdown on the first attempt at just 50 per cent.
The primary purpose of Saturday's mission was to deliver cargo to the space station, a $100-billion laboratory that flies about 260 miles (418 km) above Earth.
The capsule is loaded with more than 5,100 pounds (2,300 kg) of food, supplies and equipment, including an instrument to measure clouds and aerosols in Earth's atmosphere.
SpaceX is one of two companies hired by NASA to fly cargo to the station following the retirement of the space shuttles in 2011.
However, the second firm, Orbital Sciences Corp., was sidelined in October after its Antares rocket exploded minutes after liftoff.
Saturday's launch was SpaceX's 14th Falcon 9 flight and the fifth of 12 planned station resupply missions under its $1.6 billion contract with NASA.
The launch had been scheduled for last on Tuesday, but was called off less than two minutes before liftoff due to a technical problem with the rocket's upper-stage motor