Travel website Booking.com has apologised and offered some hotel operators cash compensation for leaving hotels and partners out of pocket for months, but those who have been left out of the payment say it adds insult to injury.

In an email sent out to hotel operators this week, the Booking.com chief executive, Glenn Fogel, apologised for “the impact that our finance and payment systems maintenance and the resulting delay in payments may have had on you and your business”.

If a customer makes a booking for a hotel through Booking.com and elects to pay upfront, the site takes the payment and passes it on to the hotel operator, minus a commission. While Booking.com continued taking payments from customers, the company did not always pass on the amount owed to hotel operators and others.

Guardian Australia reported last month that Booking.com’s partners reported issues receiving payments worth thousands of dollars – or the equivalent in other currencies – since July, and in some cases months earlier.

Fogel said in the email that as part of making system upgrades to the company’s financial and payments platform, there were “a number of unforeseen problems” that resulted in payments being disrupted.

“We know that for some of you who were affected, this had an impact on your businesses, and on your professional and personal lives. For this, I am deeply sorry,” he said.

Fogel said partners whose payments were delayed more than 21 days would be given a “gesture of goodwill in the form of a one-time cash payment”. The 21-day delay would not include an initial 10-day freeze the partners had been warned about.

Jacqueline Stuart, who books out her holiday home in Italy through Booking.com, received the email from Fogel that included the apology, but the correspondence stated she “did not currently qualify for this goodwill gesture”.

Stuart said the company had been two months late for payments for her in June and July this year. She did not understand why she had been deemed ineligible and the email did not give a reason.

“What an insult,” she said in an emailed reply to Booking.com shared with Guardian Australia.

“Shocking, shocking customer service, which has only been made worse by this latest email.”

A spokesperson for Booking.com would not say how much money the partners would be paid or the number of partners receiving the payment.

“The exact amount of compensation for each partner will be determined by the amount owed and the length of delay experienced,” the spokesperson said.

It is understood the system in question is an SAP enterprise resource planning system, but both Booking.com and SAP had previously refused to comment on this aspect.

Late last month, Booking.com customers also reported being targeted by scam emails from Booking.com for bookings they had made, asking them to confirm their hotel payment or risk having it cancelled.

Booking.com denied its systems had been hacked, instead stating that hotel operators had their own accounts compromised through phishing attacks.