The key contractor involved in the HealthCare.gov website warned the Obama administration there were problems with the site just weeks before the Oct. 1 launch date, a confidential report reveals.

Fox News obtained a copy of the September report Tuesday night, which states the status of some areas of the website were “TBD,” and that the contractor, CGI, was unclear if those "open issues" and "open risks" would be ready for the Oct. 1 rollout. However, other areas in the report were listed as “on track.”

Some of the problems cited include that “hub services are intermittently unavailable” and time frames for testing “are not adequate to complete full functional, system, and integration testing activities.”

The report was also released by the House Oversight and Government Reform Committee, after it was given to the committee in response to their request to CGI for more information about the development of Healthcare.gov.

Obama administration officials downplayed the report, which was first reported by CNN, to Fox News, saying the CNN story cherry-picks a couple of points in the report and makes the situation seem worse than it actually was.

“This report is not a dire warning, but more plausibly a list of things to do if you read it in full – what’s been done, what needs to be done, what needs to be resolved,” a spokesman for the Center for Medicare and Medicaid Services told Fox News. “It is misleading to cherrypick a few lines.”

The report also seems to contradict testimony given on Sept. 10 by Cheryl Campbell, the CGI official who testified last week before the House, that the website had met all its major milestones in the run-up to Oct. 1.

“At this time, CGI Federal is confident that it will deliver the functionality that CMS has directed to enable qualified individuals to begin enrolling in coverage when the initial enrollment periods begin on October 1, 2013,” Campbell said at the time.

The problem-plagued website went down Tuesday night, its second outage in three days.

The Centers for Medicare and Medicaid Services confirmed to Fox News that the federal data services hub and the HealthCare.gov marketplace application were affected by the network outage, and maintenance was being performed overnight to fix the problem. 

Fox News' Ed Henry contributed to this report