The Labour leader moved Eagle to shadow culture secretary, mostly because she disagreed with his position opposing the Trident nuclear weapons system.
However, Corbyn decided to retain his shadow foreign secretary, Hilary Benn, after coming to an agreement on their future working.
The deal means there will be no repetition of their disagreement about the vote on bombing Syria, during which Corbyn argued against military action and Benn gave a speech in favour. All future positions on foreign policy will be directed by Corbyn, a Labour source said.
As well as replacing Eagle, Corbyn sacked his shadow culture secretary Michael Dugher and shadow Europe minister Pat McFadden for what Labour sources said were displays of “incompetence and disloyalty”.
McFadden is being replaced by Pat Glass, who chairs Labour’s pro-EU group. Emma Lewell-Buck gets a promotion to shadow devolution minister.
In a statement, McFadden said he had originally accepted the post because the EU issue was of “crucial importance” with an in/out referendum looming.
“Tonight Mr Corbyn has told me he does not want me to continue to serve on his front bench, in particular because of questions I asked about terrorism and national security in the Commons statement following the Paris terrorist attacks,” McFadden said.
“It is his prerogative to decide his frontbench team and I will continue to support and work for Labour in any way I can. I hope Labour retains its strong and clear position to campaign for the United Kingdom to remain in the EU.”
The developments were revealed by Labour sources in the early hours of Wednesday morning, more than 30 hours after Corbyn began his reshuffle.
The sources insisted Eagle was keen to move to the shadow culture role from defence and was happy with her shift sideways.
Corbyn had wanted to move both Eagle and Benn, but up to 10 shadow cabinet ministers threatened to resign if the shadow foreign secretary were to be moved.
Thornberry was appointed because her views on the issue of defence are felt to overlap more with Corbyn’s. It marks her return to the shadow cabinet after she was forced to resign from her role as shadow attorney general under Ed Miliband for tweeting a picture of a white van and St George’s flag, an action that was interpreted as snobbery.
Labour sources made clear that open dissent against the leader would not be tolerated in future and there would be no repeat of the situation in which Corbyn and Benn argued different positions over Syria from the front bench.
A Labour source said some shadow ministers had “got into the habit” of attacking the leadership and the reshuffle did not contradict the new politics of allowing debate.
The decision to retain Benn will disappoint some of Corbyn’s allies who have warned that the shadow foreign secretary will be at the centre of future rebellions like the vote over Syria if he remains in his post.
One Labour MP said Benn would be a figurehead for repeated shadow cabinet rebellions if he was not removed from the high-profile position.
It is understood there are still more shadow junior ministerial announcements to come but the shadow cabinet movements are now concluded, with 17 women and 14 men in top jobs.
Labour sources said Dugher was removed from his job over his disloyalty, including warnings against a “revenge reshuffle” and criticisms of Stop the War and Momentum, the grassroots group of Corbyn supporters.
They pointed to McFadden’s comments in the House of Commons about the Paris attacks as the reason for his sacking, suggesting they were a “coded attack” on the leader.
McFadden had asked David Cameron to reject the view that terrorist acts were always a response or a reaction to what the west did and to agree that such an approach risked infantilising terrorists when the truth was that they were adults, entirely responsible for what they do,
However, the Labour sources said it was not the only reason for moving McFadden, who had more recently warned Corbyn against conducting “a revenge reshuffle”.
In a parting swipe, Dugher said he had chosen to speak out because he was “frustrated and angry” at members of Corbyn’s team for briefing the press against other members of the shadow cabinet in a way that amounted to a “terrible trashing of people’s reputations”.
“I thought that was hugely damaging,” he said. “I thought it was really unfair on those people.”
Shadow cabinet ministers including the deputy Labour leader, Tom Watson, and the shadow home secretary, Andy Burnham, bemoaned the loss of Dugher, saying he was a strong campaigner who was vital for winning back working class Labour support in the north of England.
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