By Charles Ornstein

A new problem has emerged with the federal government's Open Payments system, which is supposed to go live Sept. 30 and disclose payments to physicians by pharmaceutical and medical device companies.

A couple weeks ago, the U.S. Centers for Medicare and Medicaid Services said it would be withholding information on one-third of the payments, citing data inconsistencies in company submissions.

Now, a source familiar with the matter tells ProPublica that CMS won't disclose another batch of payments: research grants made by pharmaceutical companies to doctors through intermediaries, such as contract research organizations. In these cases, doctors apparently have not been given a chance to verify and dispute payments attributed to them, as required by law.

Officials at CMS have not publicly disclosed anything about this latest batch of withheld data and did not answer questions from ProPublica about how many records are involved.

The data is required to be disclosed under the Physician Payment Sunshine Act, part of the 2010 Affordable Care Act. Sen. Charles Grassley, R-Iowa, one of the main proponents of the law, expressed frustration with the reporting system's troubles.

"CMS has had more than four years to figure everything out," Grassley said in a statement Thursday. "It's disappointing and irresponsible that so many basic questions are unresolved at this late stage."

The idea behind the Open Payments database is straightforward: Provide consumers with transparency and context about doctors' financial relationships with pharmaceutical and medical device companies.

But the effort to make drug and device payments public has been beset with delays. The Sunshine Act called for CMS to propose regulations governing disclosure by Oct. 1, 2011 and for payments to be released by the end of September 2013.

But CMS did not release its proposed rules until December 2011 and did not release them in final form until February 2013. At that time, the agency said the first release would include payments to physicians from Aug. 1 to Dec. 31, 2013. This includes payments for research, promotional speaking, consulting, meals, travel and gifts.

As information has trickled out about glitches with the database, officials at CMS have yet to answer such basic questions as how many records have been reported by companies, how many are being withheld, how many companies reported wrong data. The agency also has not specified which data is flawed and how consumers will be informed when information is withheld.

In a note to doctors earlier today, CMS said its actions to withhold records protects the integrity of physicians' data. It said it has removed records when a physician's name, national identification number and medical license number did not exactly match other official data sources.

"There will be a new time frame for the resubmission of the corrected records and a different public display date. More information about this process and timing is forthcoming in the coming weeks," the note said. CMS had previously said that the withheld data would not be made public until June 2015.

In another note today, CMS said it would give doctors until Sept. 10 to check the payments that would be attributed to them and contest them if they found problems.

Officials at the Pharmaceutical Research and Manufacturers of America, the industry trade group, said that their member companies have received little information about what is going on. Assistant General Counsel John Murphy said in a news release Tuesday that companies have been unable to find any inconsistencies in the data CMS had earlier announced it was withholding.

PhRMA spokeswoman Jennifer Wall reiterated that today.

"Our companies continue to review the data issues surrounding the recent actions by CMS to remove certain information from open payments," she said in an email. "To date, they still do not have a full accounting of the rationale behind CMS' decision and therefore it is difficult for us to fully understand the ongoing data validation issues. We look forward to working with CMS prior to the September deadline to resolve our outstanding concerns."

Many organizations, including the American Medical Association, have called upon CMS to further delay the release of the data, citing widespread confusion, poor communication with physicians and poor functioning of the website CMS set up for physicians to verify their data.

ProPublica has been tracking payments from pharmaceutical companies to doctors since 2010 in our Dollars for Docs news application. The site shows payments by companies that have made this information public, typically under settlement agreements with the government to resolve allegations of improper marketing. Dollars for Docs currently lists $2.5 billion in payments through 2012 from 15 companies representing about 43 percent of U.S. drug sales.