Hundreds of service personnel deployed throughout the Middle East to provide vital support for troops in Iraq and Afghanistan are being denied the Ministry of Defence's tax-free operational allowances, The Herald can reveal.

The move to limit payment of the £2320 "operational danger, separation and hardship bonus", introduced for service personnel spending six months away from home in combat zones, has emerged from an MoD instruction to commanders issued on November 2.

Under the rules, those "within the geographical boundaries" of the two countries, flying over them or inside Iraq's territorial waters qualify, but the chain of logistics specialists and RAF ground crews deployed to surrounding states do not.

This follows "a six-monthly review of qualifying locations" by the UK's tri-service Permanent Joint Headquarters at Northwood, Middlesex, late last year.

The change also covers the payment of £140 made to service personnel deployed for six months and who would normally pay council tax at home, though this is not thought to be a huge number.

Even within the new structure, however, there are inconsistencies. While the letter states that personnel about to relocate from Basra to Camp Beuhring, the main supply base in Kuwait, will still receive the allowance, "other service personnel deployed to Kuwait will not".

Liam Fox, the shadow defence secretary, described the policy as "shambolic", adding: "Rather than a fair remuneration package that supports all personnel deployed in support of both Operations Telic (Iraq) and Herrick (Afghanistan), including those in Kuwait and wider Gulf region, the government has produced an inconsistent, incoherent mish-mash," he added.

An MoD spokesman said: "There is no confusion. The allowance was introduced to compensate for an element of personal danger. The people at Camp Beuhring in Kuwait being paid the allowance are deemed to be in an overwatch role and could be sent back to Iraq if the situation called for it. While we recognise the vital role of ground crews and others in Qatar and in Oman, they're not in immediate personal danger."

Under the rules, sailors on warships can claim the daily rates while they patrol the area of the Gulf adjacent to Iraq. Nimrod surveillance aircraft crews flying out of Oman begin to earn the allowance when they cross into Afghan airspace.

The MoD announced the operational allowance in October, 2006, and increased it from £12.31 a day to £12.75 last June as "a way of recognising the increased and enduring nature of danger facing service personnel".

Des Browne, Defence Secretary, said: "We can't underestimate the tremendous work they are doing in Iraq and Afghan-istan when separated from their loved ones."

An RAF officer last night described the revised rules as "utterly nonsensical" and added: "The ageing Nimrods and Tornados would not be flying missions if it were not for the dedication of ground crews living in some discomfort at remote desert bases. It's not as if this saves the MoD much. It's perhaps £500,000. Are they really that broke?

"They can squander billions on procurement blunders, but seem to have no concept of how to foster the goodwill of their most valuable asset, their servicemen and women."