Clearances of ancient woodlands for HS2 must be paused until an independent review of the £88bn high-speed line is delivered, the government has said.

However, clearances deemed absolutely necessary to avoid major costs and impacts on the construction schedule can still go ahead, the Department for Transport said.

The transport secretary, Grant Shapps, told HS2 Ltd to review its programme to assess what woodland removal could be halted until after the Oakervee review, which is expected as early as next month.

It is not clear how much woodland clearance is already under way. The Woodland Trust said HS2 was planning to start work on 11 sites this autumn, including eight small woods in Warwickshire and three in Staffordshire, of between 0.1 and 3.2 hectares (0.25-7.9 acres). The biggest two are near Kenilworth in Warwickshire, South Cubbington and Broadwells Woods, home to buzzards, woodpeckers, bluebells and fly agaric fungi, according to local online reviews.

Shapps said he recognised the concerns of local residents and campaigners that irreversible work could be undertaken in woodlands while the future of the project remained in doubt. The government has promised a “go-or-no-go” decision on HS2 by the end of the year. HS2 Ltd is continuing with other preparatory works.

Shapps said: “There is no sense in hiding the challenges HS2 faces, or masking the difficult decisions that need to be taken.

“So, as Douglas Oakervee’s review continues, we must take a sensible approach and recognise that some works simply cannot be undone later.

“Having listened to the concerns of affected residents and parliamentary colleagues, I have ordered HS2 Ltd to consider what works affecting ancient woodland clearances can be delayed for the duration of the review.”

He added: “This ensures we avoid irreversible decisions without major impacts on cost and schedule. HS2 may be a complex project overall, but I think this request is just common sense.”

Luci Ryan, an ecologist at the Woodland Trust, said: “This is a welcome step in the right direction for our ancient woodlands, but unfortunately these woods remain threatened as HS2 can still decide for themselves whether works continue or not. Until the outcome of the review all ancient woodlands should be off limits, full stop. Our welcome is therefore cautious.”

According to the Woodland Trust, up to 108 areas of ancient woodland are likely to be affected should the entire HS2 route go ahead. While HS2 has said it will plant more trees and create four times more woodland than is taken for the railway, the charity says that England’s ancient woodlands constitute “highly complex ecological communities that have developed over centuries” and cannot be moved or replaced.

The Woodland Trust argues that many species of flora, fauna and fungi which rely on the sites for survival, including woodpeckers, bats, dormice, otters and hedgehogs, are threatened by the plans.

An HS2 Ltd spokesperson said: “We are committed to reducing the new high-speed railway’s impact on ancient woodlands. As highlighted by the secretary of state, we must strike a sensible balance between keeping the programme on track, and recognising that some works cannot be undone.

“We are working with the Department for Transport and our contractors to assess these areas and their impacts while the review is ongoing.”

HS2 said only 43 of 52,000 ancient woodland sites in England would be affected on the route between London and Crewe, and over 80% of the total area of those 43 sites would remain intact and untouched.

It has pledged to mitigate the effects of construction by creating a “green corridor”, planting 7m trees between London and Birmingham and adding 33 sq km (13 sq miles) of wildlife habitat during the first phase of construction.

The Oakervee review, led in conjunction with prominent critics of the scheme, is expected to assess the costs and benefits of HS2, and could recommend a modified version of the railway, such as running slower trains or changing its London terminus.

Earlier this month, the government revealed it expected HS2 to be delayed by five to seven years, and to run another £26bn over budget, revising its price up from £56bn in 2015 to £88bn, in line with inflation.

Based on a report from the HS2 chairman, Allan Cook, it said the first phase from London and Birmingham would probably not be ready until 2031, instead of 2026, while the entire network including lines to Manchester and Leeds might not be completed until 2040, instead of 2033.