A spokesperson for A-Rod, who is on the disabled list while rehabbing from hip surgery, "flatly denied the allegations."
A source told the Times that MLB, which does not have subpoena power, was simply fighting fire with fire, making every effort to obtain evidence in an atmosphere in which investigators believed that players were also trying to buy records.
The Times report quoted two sources saying that former Biogenesis employees who have cooperated were compensated for their time. The payments "were not believed to have exceeded several thousand dollars."
Pat Courtney, MLB's senior vice president of public relations, said that it is MLB's policy not to comment on ongoing investigations.
The Times story noted, "That baseball is paying for evidence underscores just how determined it has become in trying to establish what went on at [Biogenesis]."
The first public allegations surfaced in January when the Miami New Times reported that it had possession of medical records that tied several stars -- Rodriguez, Melky Cabrera, Gio Gonzalez, Bartolo Colon, Nelson Cruz and Yasmani Grandal among them -- to human growth hormone and other banned substances. Later, 2011 National League MVP Award winner Ryan Braun was also implicated. All who were named have denied any wrongdoing.
The New York Times report continued: "But the denials have essentially been brushed aside by baseball and its investigators, who remain intent on obtaining whatever testimony and evidence they can in connection with the clinic's activities and determining whether they then have grounds to discipline players even in the absence of a positive drug test.
"Indicative of Major League Baseball's resolve in this case, Commissioner Bud Selig sent two of his top deputies -- [executive VP of economics and league affairs] Rob Manfred and Pat Courtney -- to Florida in February to try to convince the Miami New Times to share the documents they had obtained. The newspaper declined."
When MLB filed a lawsuit against six individuals with connections to Biogenesis last month, it was seen as a move in part to try to give investigators the right to subpoena records and compel depositions.
Paul Hagen is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.