The former Ukip leader criticised Mr Carswell for “not wanting” to discuss immigration when the debate had yet to properly begin.
The pair have clashed in the past, including over the Clacton MP’s more liberal stance on immigration which has put him at odds with some of the party’s top ranks.
Mr Farage delivered his swipe after giving a fiery speech at the Ukip Spring Conference in Bolton on Friday.
Nigel Farage criticised Douglas Carswell for ‘not wanting’ to discuss immigration
The leader insisted Ukip remain a “radical force” in Britain and not become another mainstream, Westminster-centric party.
“There are too many people in Ukip… who are now urging Ukip to become mainstream,” he said as the crowd shouted “no” in a disapproving tone.
“It’s nice to be popular, it’s good to get invited to all the right social event parties in London and I guess it’s easier in life to be thought of as nice rather than one of those unpleasant populists.
His swipe came after he gave a speech at the Ukip Spring Conference in Bolton on Friday
“But this attitude is not Ukip. Ukip is a radical party or it is nothing."
I don’t think the debate on immigration has even begun
After his speech, Mr Farage was asked if Mr Carswell, who defected from the Tories to Ukip in 2014, was radical enough for Ukip.
“Is he in Ukip?” the 52-year-old sarcastically responded.
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“Douglas Carswell takes a completely different view to me, it’s obvious.
Nigel Farage in pictures
Thu, December 15, 2016
Nigel Farage is a British politician who has been the leader of the UK Independence Party since October 2016.
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British politician Nigel Farage arrives at Trump Tower on December 15, 2016 in New York City. President-elect Donald Trump and his transition team are in the process of filling cabinet and other high level positions for the new administration.
Mr Farage was asked if Mr Carswell was radical enough for Ukip
“He thinks we shouldn’t talk about immigration, I don’t think the debate on immigration has even begun.”
The MEP said it was now up to the party’s new leader Paul Nuttall to clarify Ukip’s immigration stance.
He said: “It ain’t my choice, it’s not Douglas Carswell’s choice, it’s Paul’s choice as to where he steers the ship.
“But, there are two competing views on this.”
Although an avowed eurosceptic, Mr Carswell, who did not attend the conference and instead delivered a recorded message, has previously been accused of trying to “split” Ukip.
In the wake of the 2015 general election – where the party failed to gain a single seat despite winning close to four million votes – he criticised Mr Farage's behaviour and strategy during the campaign.
He said the party should “take positions on things like immigration and Europe, but not bang on obsessively” about them.