Union chief executive Dale Cobb said iwi were disappointed.
"The Americans were a bit nervous about the river journey - they felt there was some risk," Mr Cobb said.
"It may be something some of them are not used to.
"We will still be providing an opportunity for the public to engage with the US party along the riverbank - we are looking at alternatives," said Mr Cobb, admitting that time was short.
The Americans, who fly into Wanganui on September 3 and who will base their pre-World Cup preparations at Cooks Gardens, say their decision did not reflect any disrespect for Maori culture.
Michelle Hooper of Rugby New Zealand 2011, the World Cup organising body, said: "Activities of this nature can only be undertaken by teams with the implicit approval of the team manager on behalf of the team for safety and security reasons.
"The USA team manager did confirm with their team liaison officer that they did not wish to go on the waka on the river.
"They do not mean any disrespect by this."
Whanganui iwi representative and Wanganui District Council Maori liaison officer John Maihi said he wanted to hear the official word on the matter for himself.
"My position is that we've never given up on anything else before, we'll probably challenge them."
He said he expected Maori Affairs minister Pita Sharples, Maori Party co-leader Tariana Turia and Wanganui MP Chester Borrows to "make a ruckus" if the US pulled out.
Meanwhile, Rugby World Cup organisers are hoping a strong showing by Australia will entice more Wallaby fans across the Tasman and push ticket sales to the $268 million target.
Rugby World Cup Minister Murray McCully said yesterday he was comfortable with how sales were tracking, and they were "pretty much on target".
But with 16 days to go until the start of the 42-day tournament, ticket sales were $30.5 million short of the target.
If ticket sales reach the target, New Zealand will still lose $39 million - shared by the Government and the NZ Rugby Union.
About 450,000 tickets worth $60 million were still available yesterday.
Mr McCully last night went to Australia for three days to try to spark more interest in the tournament.
He said that since the last update a fortnight ago, 20,000 tickets worth $4 million had been sold.
Mr McCully also said the Australian and England squads had each planned a day of activities in Christchurch to support the earthquake-ravaged city.
Both teams were going to base themselves in the city during the tournament before the earthquakes struck.
