The Welsh Assembly member followed his close friend Douglas Carswell in leaving the anti-Brussels party to become an independent.
He pledged to sit with the Tory group in Cardiff but insisted he was not re-joining the Conservative Party.
Angry Ukip officials described his defection as "disappointing" and urged him to quit the assembly today.
And former party leader Nigel Farage said: "I have always liked Mark Reckless, but if he thinks he can just leave after being elected on a list system that is very dishonourable behaviour.
Nigel Farage has launched a blistering attack on twice-defectee Mr Reckless
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If he thinks he can just leave after being elected on a list system that is very dishonourable behaviour
"He is clearly close to Douglas Carswell, I guess some kind of pressure’s been put on him."
Mr Reckless caused a sensation three years ago when he followed Mr Carswell in defecting from the Tories to Ukip.
He won a subsequent by-election to stay on as Ukip MP for his constituency of Rochester and Strood but then lost the Commons seat to the Tories at the 2015 general election.
He has since been Ukip's head of policy and was elected to the Welsh Assembly last year.
Announcing his resignation from Ukip, Mr Reckless praised the "exemplary" leadership of Theresa May.
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The news comes after Mr Carswell stepped down from the Party
Ukip described the move as "disappointing" and called on him to stand down from the assembly.
In a statement, Mr Reckless said: "Since being elected to the assembly in May I have been thoroughly impressed by the performance and discipline of Andrew RT Davies and the Welsh Conservative group.
"The Prime Minister's leadership since taking office has also been exemplary and she has been steadfast in her position to deliver on the wishes of the people of Wales and the United Kingdom, building a united country that works for everyone and not just the privileged few."
Ukip chairman Paul Oakden said that as Mr Reckless had been elected through the party list system – which meant voters were voting for the party rather than individual candidates – he should give up his seat for a Ukip candidate.
He said: "Having been elected as a Conservative in Rochester and Strood, Mark didn't think it right to sit as an MP for another party without asking the electorate for their endorsement in a by-election.
Mr Reckless praised the "exemplary" leadership of Theresa May
"A position that was as right as it was honourable.
"It is now incumbent on Mark Reckless to relinquish a position he has only by virtue of a Ukip mandate.
"The position should go to the next Ukip candidate on the regional list."
The Tory group in Wales confirmed that while Mr Reckless had joined the party's group in the assembly – making them the second largest party after Labour – he had not actually re-joined the party.
In a letter to the Welsh Tories' leader Andrew RT Davies, the assembly presiding officer Elin Jones said that as Mr Reckless was no longer a member of Ukip, that he "can be treated as a member of your group for the purposes of our procedures within the assembly".
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A Tory spokesman said: "Decisions about who sits with the Conservative group in the Welsh Assembly are a matter for the group in the Welsh Assembly."
Mr Reckless's decision to side with the Tory group in Wales was warmly welcomed by Mr Davies.
"Mark's decision to join the group is testament to the strength and unity of the Welsh Conservative team in Cardiff Bay which provides the only real opposition to a tired and complacent Labour administration."
A spokesman for the Ukip group in the Welsh Assembly said: "This defection is a slap in the face for the voters of South East Wales who voted for Ukip in 2016 in the good faith they were electing a Ukip Assembly Member.
"If Mark Reckless has any sense of honour he will resign his seat without delay and stand by the commitment he gave in 2014 when he defected from the Tories – namely not to switch parties without the consent of his constituents.
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"As was the case with Nathan Gill, Ukip were elected through a proportional list system.
"Neither Mr Gill nor Mr Reckless have a democratic mandate to remain in the Assembly. Both should resign and allow Ukip to nominate local members to take their place.
"As we commence Brexit negotiations, the people of Wales need to know now, more than ever, that their interests will be protected.
"Ukip is the only party in the Welsh Assembly committed to a complete withdrawal from the European Union. It is therefore vital that there is a strong Ukip voice in the Assembly.
"Ukip received four million votes in the last general election – more than the SNP and Liberal Democrats combined.
"In a few months this will be history and we will go on representing the hard-working people of Wales, with or without Mark Reckless in the group."
Mr Reckless's decision to re-join the Conservatives means they overtake Plaid Cymru as the second largest party in the Assembly, making them the official opposition to Labour.