The BBC has received 517 complaints since the show aired on Sunday, which featured Clarkson and his co-presenters Richard Hammond and James May completing a set of tasks in HGVs.
As Clarkson drove one of the HGVs, he said to the camera: "What matters to lorry drivers? Murdering prostitutes? Fuel economy?
"It's a hard job and I'm not just saying that to gain favour with truck drivers. There's so much to do.
"You've got to change gear, change gear, change gear, check mirror... murder a prostitute. Change gear, change gear, murder."
His remarks were an apparent reference to the Yorkshire Ripper Peter Sutcliffe, a lorry driver, and Suffolk Strangler Steve Wright, who was a former forklift truck driver.
A BBC spokesperson said: "The vast majority of 'Top Gear' viewers have clear expectations of Jeremy Clarkson's long-established and frequently provocative on-screen persona.
"This particular reference was used to comically exaggerate and make ridiculous an unfair urban myth about the world of lorry driving, and was not intended to cause offence."
The joke was not received well by some lorry drivers, including Roger King, chief of the Road Haulage Association.
King wrote to the BBC: "While this could be interpreted as being 'humorous', it certainly is not seen that way by over half a million lorry drivers."
However, one of the UK's biggest haulage firms, the Eddie Stobart group, threw its support behind Clarkson.
Andrew Tinkler, chief executive of the group, said: "They were just having a laugh. It's the 21st century, let's get our sense of humour in line."
Will Shiers, the editor of Truck & Driver magazine, also came out in support of Clarkson.
Shiers said: "[The] bulk of the UK's drivers who saw the programme loved it. Yes, a small number of drivers were offended by the murdering prostitute reference, but they really are in the minority.
"On the whole I thought the show was really entertaining. If anything it succeeded in demonstrating to car drivers just how difficult it is to drive a truck."
Ofcom said it had received complaints and was "looking into" the incident but that it had not launched an investigation.
The TV watchdog could not verify the number of complaints it had received.
During the 'Top Gear' episode on Sunday, Clarkson drove his HGV through a brick wall at about 90km/h to complete one of the set tasks.
Clarkson's cab crumpled as the truck hit the brick wall, leaving him with a heavily bruised shin and back, and an index finger that looked like "a burst sausage".
These fresh complaints come just days after the BBC was forced to discipline Jonathan Ross for the lewd phone calls he and comedian Russell Brand made to 'Fawlty Towers' actor Andrew Sachs.
Brand resigned from his BBC Radio 2 show early last week, while Ross was suspended without pay for 12 weeks, taking a £1.3m chunk out of his £6m per-year pay packet.
Lesley Douglas, the BBC Radio 2 controller, also resigned as a result of the incident.