HMRC wants staff to travel to the lavish London venue - more used to royal weddings, coronations and state funerals - to listen to hymns and readings about its "core purpose".
SNP Treasury spokesperson Stewart Hosie criticised the decision.
The Public and Commercial Services Union (PCS) has estimated that more than 34,000 jobs have gone from HMRC since 2005, while staff have also taken industrial action recently over more losses.
In 2012, relations between management and their workers were so fractious that a senior HMRC figure suggested a "truth and reconciliation" process was required.
However, next month's "thanksgiving" service is intended to help staff feel good about the public body.
A briefing states: "The aim of the service is to celebrate the vital work that we do in HMRC to collect revenue to fund public services and to benefit society as a whole."
The events will consist of "testimonials, readings and hymns all reflecting the core purpose of HMRC".
Around 1500 people from across the department are expect to attend. HMRC has large Inland Revenue offices in East Kilbride.
Eyebrows have been raised about the appropriateness of the service and its opulent location. Westminster Abbey, a Gothic masterpiece, is more famous for events such as the funeral of the late Princess Diana.
HMRC is not being charged for its use of the venue, but a spokesman confirmed there would be costs for "staff time".
HMRC will use taxpayers' money, however, for travel and subsistence for those who attend.
In 2010, a study on public service satisfaction by watchdog Consumer Focus ranked the tax office 18th out of 23.
The National Audit Office recently revealed that HMRC had overestimated the amount it had collected in tax by nearly £2 billion, a miscalculation senior Labour MP Margaret Hodge said was a "serious error".
John Davidson, who is a member of the PCS Scotland committee, said: "At a time when HMRC are getting a real-term pay cut and jobs are under threat, this thanksgiving service shows how out of touch management is. It's wasteful and insensitive."
An HMRC spokesperson said: "A shared sense of purpose is key to boosting staff morale. The ongoing improvement to the quality of service we provide to the public will be supported by the recognition at this event of the vital role HMRC people play in society. It is for followers of all faiths and none."
Hosie said: "It's not surprising that PCS, which represents HMRC workers, thinks the service is wasteful and insensitive.
"Perhaps HMRC should instead spend time reflecting on how to introduce a living wage."