John Witherow was giving evidence to an employment tribunal in which transgender woman Katherine O’Donnell is suing The Times for alleged unfair dismissal and discrimination.
The former night editor of the Scottish edition of The Times was made redundant in January 2018, after 14 years at the newspaper group.
During lengthy cross-examination at the hearing in Edinburgh on Friday, Mr Witherow was shown dozens of examples of stories and columns published in The Times on which he was questioned by Ms O’Donnell’s lawyer, Robin Moira White.
Mr Witherow admitted that, in a Christmas-themed satirical column by Giles Coren, a gag about people who were “something in between” men and women, should have been cut.
“It’s not a very good joke and it probably shouldn’t have stayed in, but some things slip through,” he said.
The Times editor was also asked whether the headlines of several articles accurately reflected the content of the story, as required by the Editor’s Code of Practice.
Asked whether a piece by columnist Janice Turner titled “Children sacrificed to appease trans lobby” was appropriate, Mr Witherow replied: “Yes, I think it backs up what she is saying.”
Mr Witherow strongly defended the paper’s reputation as “the paper of record”, and said: “There is not any trans bias in The Times.
“There is quite a lot of stories picked out, over a couple of years, but we publish about 60,000 stories a year.
“Not all are outstanding pieces of journalism but most are.
“We take great care in getting things right, in being good reporters.”
However, shown a story centred on perceived fears about trans people sharing rooms on the Caledonian Sleeper train, Mr Witherow told employment judge Jane Porter “If I had seen it, I would have spiked it.
“It doesn’t seem like much of a story.”
The hearing continues.