Keegan has resigned from the club after just eight months on Thursday evening following a disagreement with the club's directors.
It is believed that Keegan brought to an end his second managerial stint on Tyneside because he was frustrated by the club's transfer policy
But Newcastle insist they gave the former England chief the opportunity to voice his concerns before he walked away.
A statement on the club's official website read: "Newcastle United football club is sad and disappointed that Kevin Keegan has resigned.
"Over the last few days the club has devoted itself to the discussions it has held with Kevin and as a result of those discussions had put together a set of practical suggestions for how to move forward.
"Today the club made it clear to Kevin that if he had any outstanding concerns on its proposals, he should raise them with the club.
"The club regrets that Kevin has, instead of taking up that offer, chosen to resign."
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