In a response to the Scottish Government's consultation on the future management of the diseases, the NTS said treating individual outbreaks as "hot spots" in isolation could lead to the loss of historic plant collections.
Currently, a 2m buffer zone has to be cleared around infected plants within 30 days and all debris has to be burned.
The diseases have infected four NTS gardens in western Scotland. P. ramorum has been found at 43 sites in Scotland and several hundred in England and Wales. P. kernoviae has hit southern England, Cheshire and Wales, and has been in Scotland since January.
The NTS is concerned that historic landscapes and important plants are being lost before heritage impact assessments and propagation can take place.
Head of gardens and designed landscapes services Jan Haenraets said: "Rather than using the present 30-day 'hot spot' approach for each site, a range of measures must be developed that take the scale of the outbreak and site-specific concerns into consideration. There is a real risk that, in the long term, this approach could cause irreversible damage to important historic landscapes. In some cases it does not give gardeners sufficient time to undertake the required measures."
The charity has asked the Scottish Government to compensate nursery businesses and landowners who have to destroy plants. It said more investment in research is needed, along with more inspectors to test for the disease and map its presence across Scotland.
Defra and the Forestry Commission share responsibility for managing Phytophthora in England. The Scottish Government and Welsh Assembly share responsibility with the Forestry Commission in their respective areas.
The Phytophthora Programme Board, which includes Defra, the Forestry Commission and the Scottish and Welsh governments, is responsible for co-ordinating action against the diseases.
The Scottish Government's consultation on future management of the disease closed on 7 October. Defra also conducted a consultation, which closed on 10 October.
Both documents offered two options: one proposing minimal control and the second proposing increased eradication measures. The Scottish approach also listed a third option - a further two years of the current level of containment and eradication activity while more evidence is gathered.
A decision is expected by next spring.