The party said charity-funded research has been severely impacted by Covid-19, with charities projecting it will take more than four years for spend to recover to normal levels.
Only five of 152 medical research charities (3 per cent) are eligible for Government support, it claimed, adding that charity funding for medical research has plunged by 41 per cent.
Important medical studies said to be stalled or cancelled include those tackling dementia, coronary heart disease and cancer, which could have long-term consequences for patients.
Labour is warning that with around half of all medical research spend coming from charities, the impact on scientific progress could be stark.
Chi Onwurah, shadow minister for digital, science and technology, said: "The UK gets great returns on research funding, both in terms of our economy and in the positive impact for those that rely on breakthroughs in treatment.
"The Government needs to urgently listen to the sector and address their concerns. Cold-shouldering these charities now will have huge ramifications down the line."
Last month, Cancer Research UK said its planned research spend over the next four to five years needs to reduce by £150 million.
It also announced plans to cut almost a quarter of its jobs, with up to 345 redundancies over the next six months.
In June, British Heart Foundation chief executive Charmaine Griffiths said it is losing £10 million a month, even with support from the furlough scheme.
A spokesperson for the Department of Health and Social Care said the government is committed to supporting research.
“So far, 27 research projects have received a share of a £25 million investment and £750 million has been given in support to the charity sector,” they said.
"We are in continuous dialogue with these charities as we assess the impact of this unprecedented pandemic, to ensure patients continue benefiting from charity-funded research."