It recommended that the Tata conglomerate, which has major share in the project, should abandon it.
However, the university which prepared information used by Greenpeace, alleges the group has "doctored" its document.
"Greenpeace has placed on its website a report under the title Biodiversity Assessment of Dhamra Port and Surrounding Areas, Orissa," said the vice chancellor of North Orissa University, Sudarsan Nanda.
"The cover page of the report says that the report has been prepared by North Orissa University.
"I would like to clarify that no report under the above mentioned title has been prepared by the North Orissa University."
Mr Nanda pointed out that the university did prepare a report about biodiversity at the Dhamra Estuary on the Orissa coast, but the contents of the Greenpeace report were significantly different.
"A comparison of the Greenpeace report as it appears on their website and the report of North Orissa University reveals that Greenpeace India doctored the authentic report of the university by way of changing the title and contents for motives best known to them," Mr Nanda said.
Professor Sushil Kumar Dutta, who conducted the assessment study as principal investigator, said the environmental impact of Dhamra Port was not included within the scope of the study.
"It was just an inventory study. However, to my surprise Greenpeace India has drawn its own conclusion on the impact of the Dhamra Port on the biodiversity of Dhamra estuary," Mr Dutta said.
The university has now threatened to seek legal action against Greenpeace.
Greenpeace has strongly reacted to the tampering accusations.
Its Oceans Campaigner, Ashis Fernandes, said that Mr Dutta was present when Greenpeace released its report on Dhamra Port in Mumbai (Bombay) on 8 June and made no complaints then.
Greenpeace says that the port project would endanger thousands of Olive Ridley sea turtles which nest on the beaches of Orissa.
"We stand by what we have observed in our report," said Mr Fernandes.
He said that his organization had "evidence to substantiate and unequivocally establish that the allegations leveled by university were baseless".
The proposed port, when completed, will be the deepest in eastern India, capable of handling vessels with a capacity of up to 180,000 tonnes.
The master plan provides for 13 berths capable of handling more than 80m tones of cargo.
The port is mainly planned to cater to the steel and aluminum industries being set up in mineral-rich Indian states of Orissa, Jharkhand and Chhattisgarh.
"We will go ahead with the port project. In fact, construction has already begun and we are keen to complete it by March 2010," the head of the Dhamra Port Company, Santosh Kumar Mohapatra, said.
"The port is being built after obtaining all necessary clearance from the relevant authorities," he said.