Mr Abe was shot dead while giving a speech at a political campaign event.
Prince William’s tribute to the former Japanese prime minister referred to the “warmth and generosity” he showed the Royal during his visit.
Wills said: “I am deeply saddened to hear of the death of former Prime Minister of Japan Shinzo Abe.
“A true statesman and devoted leader. I will not forget the warmth and generosity he showed me during my visit to Japan in 2015.
“My thoughts are with his family and the people of Japan.”
The Queen also issued a message of condolence on Mr Abe’s death and expressed her “deepest condolences” to the Japanese people.
Her Majesty said she and the family were “deeply saddened” to learn of his death.
She added: “I have fond memories of meeting Mr Abe and his wife during their visit to the UK in 2016.
“His love for Japan and his desire to forge ever closer ties with the UK were evident.
“I want to convey my deepest condolences and condolences to his family and the people of Japan at this difficult time.”