Treasurer Joe Hockey on Friday said he did not believe a 100% take-over would be in the national interest.
"We are disappointed by the government of Australia's decision," a State Department spokeswoman told the Australian Financial Review on Monday.
The US was the largest foreign direct investor in Australia, with $US132 billion (A$145 billion) in investment projects to date, it said.
"We look forward to working closely with Australia's government to build stronger trade and investment ties."
"This was a very complex case," parliamentary secretary Josh Frydenberg told Sky News, citing GrainCorp's dominant position over east coast bulk grain exports.
"It was never going to be easy to make a decision."
The ABC reports shares in GrainCorp closed at $A8.72 on Friday, down 22%, or $A2.48, following the announcement.
ADM already owns around 20% of GrainCorp. The BBC reports its bid to fully acquire the company was opposed by some farm groups, who raised concerns over the impact of such a move on competition in the sector.
