Rosenthal said deleting the e-mails was "an error in judgment" and denied it was done to avoid a court request to produce the communications.
Last month, as part of a federal civil rights lawsuit filed against the Harris County Sheriff's Department, more than 100 e-mails were briefly released that detailed an affectionate relationship between Rosenthal and his secretary, Kerry Stevens.
Rosenthal, who is married, wrote messages like "I want to kiss you behind your right ear" to Stevens. U.S. District Judge Kenneth Hoyt, who mistakenly made the e-mails public, later resealed them.
Rosenthal said he had an affair with Stevens in the 1980s when he was married to his first wife, but said the relationship did not lead to his divorce. Rosenthal said he told his current wife about the affair before hiring Stevens when he took office in 2000.
Rosenthal, facing pressure from fellow Republicans since the romantic e-mails were made public, on Wednesday withdrew his name from the March 4 primary ballot, ending his re-election bid.
On the same day, Hoyt ordered a court hearing Jan. 31 to review a request that Rosenthal and two others with the district attorney's office be held in contempt and fined for the deletion of the more than 2,500 e-mails.
Rosenthal is a witness in the 2004 lawsuit, filed by two brothers who say they were wrongly arrested by the sheriff's department while they filmed officers executing a search warrant at a neighbor's home.
As part of the lawsuit, the brothers' attorney, Lloyd Kelley, has requested copies of e-mails from Rosenthal's office. Some of the e-mails that were released to Kelley included those between Rosenthal and his secretary.
But Rosenthal deleted some 2,500 e-mails that Kelley had requested.
"Rosenthal's actions are motivated by his desire to hide potential criminal and/or immoral conduct on his part and those of his closest aides. Now, Rosenthal wants the Court to hide from public view his outrageous behavior and to simply ignore his 'bad boy' conduct and intentional contempt of this Court's orders," Kelley wrote in a court motion last month asking that Rosenthal be sanctioned.
But Rosenthal, who did not immediately return a telephone call seeking comment Thursday, said in court documents last month that he deleted the e-mails to reduce their large volume visible on his computer.
"I concede that my decision to delete e-mail was an error in judgment. I was not trying to and did not delete all the e-mails responsive to the (lawsuit)," Rosenthal wrote.
He added he believed a list of the e-mails had been printed and that even if deleted, they could still be retrieved by his technical staff. He said his office's technical team has been working to try and retrieve the e-mails.
Rosenthal has sought to prevent the public release of e-mails he sent to his secretary, saying they are protected under privacy rules.
Kelley, who did not immediately return a telephone call seeking comment Thursday, has said these e-mails aren't protected.