The remains were found in the White Sands Missile Range in the San Andres mountains by a team of searchers from UP Aerospace, which organised the flight, with help from the US military which owns the site.
The canister was lost on re-entry after its homing beacon could not be located.
UP Aerospace co-founder Eric Knight told Associated Press that the payload "landed where we wanted it to be. It was just in difficult terrain. And some days, the weather was not cooperative."
The ashes were sent aloft on 28 April for a four-minute sub-orbital flight before re-entering the atmosphere and parachuting to Earth.
This was the first ashes flight for UP Aerospace and the company is planning more launches, including leaving ashes permanently in orbit, on the moon or in deep space.
The ashes of Doohan, along with Nasa pioneer L. Gordon Cooper, who went into orbit with the Mercury and Gemini rockets and 200 others, will now be mounted on memorial plaques and returned to relatives.
"He probably wished he could have stayed in space," Doohan's wife Wende said in a telephone interview from her home in Renton, Washington.
"When Senator John Glenn went up in space [aboard the Discovery shuttle in 1998], he said that they're starting to use seniors now, and he wanted to put his name on the list."
Moon's dark side is mountainous, rugged and never visible from the Earth
The groundwater basins in some areas of Tehran have been damaged irreversibly
This is the first time that any spacecraft on Mars has recorded air vibrations on the planet
Arctic sea ice is thickening at a faster rate during winter, thus slowing down long-term decline: NASA
But, the seasonal ice growth could only delay the demise of the Arctic ice cap for a few more decades