The US Department of the Interior has criticised as "inaccurate" the State Department's draft conclusions that the impact of the Keystone XL pipeline on wildlife would be temporary, and has warned instead that it could have long-term, adversarial effects.

It is the second major government body to publicly criticise State's draft environmental impact statement (DEIS), a much contested document which examines the pipeline's potential impact on the natural environment, endangered species, communities and the economy. The DEIS, published in March, concluded that the project would only have a temporary and indirect impact on wildlife.

A 12-page letter, dated 29 April by the Interior Department's Office of Environmental Protection and Compliance and posted on the department's website on 15 August, warned that some effects of the pipeline on wildlife may be permanent.

In the letter, the Department of the Interior repeatedly takes issue with the conclusions of its fellow agency that any impact on wildlife would be short-lived and occur only during construction. The Keystone pipeline, which will transport oil-sands bitumen from Canada across thousands of miles to Nebraska, requires a presidential permit from the State Department, because it crosses the US border.

The Interior letter lists several potential permanent threats to wildlife, including "loss of habitat, habitat fragmentation, species displacement, barrier effect, etc", and says that the DEIS's conclusion that "permanent impacts are not expected" in terms of wildlife is not accurate.

One of 100,000 public comments received on the DEIS "at the same time", according to the State Department, the letter states:

"Given that the project includes not only constructing a pipeline but also related infrastructure, access roads, and power lines and substations, impacts to wildlife are not just related to project construction. Impacts to wildlife from this infrastructure will occur throughout the life of the project (ie: operation and maintenance phases)."

It also states that while the potential impact to fish and aquatic invertebrates have been included in the DEIS, "there there is no acknowledgement of the potential impacts to wildlife in the event of spills or leaks".

A spill in the North Valley Grasslands Important Bird Area or the Rainwater Basin IBA could "severely impact critical habitat for migratory birds that spend part of their life cycle on Department managed lands", the letter states.

The Department of the Interior also lists other potential impacts of the pipeline project, such as noise and light pollution, that it said the DEIS had not properly addressed.

A State official said the department was working towards a final environmental impact statement and would consider more than 1.2 million public comments received, including the letter from the Department of the Interior. In a statement, the official said: "We look forward to continuing to work with the Department of Interior on the issues described in its letter.

"The Department of State continues to review the presidential permit application for the proposed Keystone XL pipeline in a rigorous, transparent, and efficient manner."

In April, the Environmental Protection Agency described the DEIS as having "insufficient information". Specifically, it said the draft had failed to account for potentially vast greenhouse gas emissions and the risk to aquifers along the pipeline's proposed 875-mile route.

The project has been opposed by environmental groups, which say the type of oil known as tar sands is more carbon-intensive to produce than ordinary crude oil and that the pipeline would add to production.

Last month, the State Department's internal watchdog announced an inquiry in response to allegations that the consultancy picked to conduct the DEIS had financial ties to the Keystone builder, TransCanada, and the American Petroleum Institute, a Keystone supporter.

President Barack Obama recently disputed one of the key justifications for the pipeline, in comments that environmental campaigners interpreted as evidence that he was leaning towards rejecting the project.

"Republicans have said that this would be a big jobs generator" Obama said, in an interview with the New York Times. "There is no evidence that that's true." He said that his decision would be based on the impact on climate change.

David Sheremata, a spokesman for TransCanada, said that the company's application to the Department of State "shows there are detailed steps we have taken to mitigate impacts on the environment, sensitive areas, wildlife and communities".

Sheremata said TransCanada was awaiting the final EIS, and added: "There are already more than 12,000 pages of technical review that have been published on Keystone XL, and they have stated that there will be a minimal impact on environmental resources along the entire route."