SOLVING THE MYSTERY behind the slow zone takeover of the MBTA subway system is taking longer than originally expected.

The MBTA hired Carlson Transport Consulting of Woburn on March 13 to investigate what went wrong and gave the firm 90 days to get answers. That wasn’t enough time apparently because the T has now extended the contract until August 29, according to an extension agreement released by the transit authority on Monday.

Slow zones are crippling the MBTA, partly because they make trips longer than they should and partly because there’s been no explanation of what’s causing them and no timetable for eliminating them. Indeed, the percentage of track with slow zones has remained remarkably steady over the last several months despite successful efforts to remove slow zones on parts of the system.

On March 9, Jeffrey Gonneville, who at the time was serving as acting general manager of the MBTA, ordered a slowdown of trains across the entire subway system after he learned there was no documentation that track defects uncovered by scans and inspections had been repaired. Slowing trains down is a way to prevent accidents.

He then dispatched teams of engineers to find out whether the defects had been addressed, a process that allowed him to fairly quickly lift the systemwide slowdown and replace it with slow zones that currently cover 23 percent of the subway system.

Phillip Eng, who took over as MBTA general manager in April, has declined to say what caused the slow zone problem and when it will be eliminated.

The contract with Carlson Transport Consulting calls for the company to review track testing data and inspections for the last 24 months and interview past and current managers and staff of the T’s maintenance of way division, which is charged with repairing track defects.

“Evaluate all collected and reviewed materials and interview and provide summary of evaluation including opinion on root causes, failure modes, and lines of responsibility,” the contract states.

Carlson, according to the contract, will collect a fee of $300 for every hour of work. The original contract estimated Carlson would work 208 hours, which works out to $62,400, not including expenses for travel and other out-of-pocket expenditures.

The same fee structure applies for the contract extension, although the extension provides no estimate of how many hours will be needed. Ominously, the extension is called Amendment No. 1, suggesting the possibility that there may be more to come.