The notes were exchanged less than a month before armed police raided Dotcom's $30 million home in Coatesville, north of Auckland, to arrest the millionaire on United States charges of criminal copyright violation.
The details are the latest to emerge from the Act leader's Christmas trip to Hong Kong.
The holiday has already caused embarrassment for Mr Banks after he denied - then admitted - getting a discount.
Mr Banks said he had negotiated the cheaper rate with the hotel by himself. Last night he confirmed he had received a gift basket from Dotcom while staying at the Grand Hyatt.
"I did not accept the gift and gave it away to hotel staff. Out of courtesy, I wrote a note to thank him."
Mr Banks confirmed he had stayed at the Grand Hyatt, where Dotcom rented the top floor, at the recommendation of Dotcom's head of security Wayne Tempero. Emails from hotel staff after Mr Banks checked out show Dotcom was briefed on his stay.
A senior staff member at the hotel emailed to say he had "just seen Mr and Mrs Banks off".
"They had a great stay and asked me to pass on their thanks to you for your hospitality and kindness."
He wrote: "In the end Mr Banks was more comfortable paying for everything. He paid himself for a Regular room and I upgraded him to a Grand Harbour Delux room with our compliments."
The staff member reported staff had been "very attentive to their needs". He wrote that Mr Banks had left "a fine bottle of whisky as a thank you" for Dotcom, along with a note.
