The government has been asked to extend the £500 self-isolation grant to those asked to stay at home by the NHS app.
Currently people with low incomes in England can claim the lump sum if they are asked to self-isolate by NHS Test and Trace.
But those who receive a notification telling them to quarantine by the NHS app are not entitled to the same payment.
The scheme, brought in at the end of September, is intended to provide income support for those who cannot work from home and have lost income as a result of being forced to isolate.
Watch: What is the Job Support Scheme and how has it changed?
A spokesperson for Citizens Advice said the current allocation of grants was leaving scores of people across the country with an “impossible choice”
Katie Martin told BBC News: "Ultimately people are facing an impossible choice often.
"They are taking a big hit on their incomes if they can't work from home and they need to self-isolate, but they still have their bills to pay, their food shopping to do, children to care for."
The government guidance on the scheme said: "Further work is needed to determine if it will be possible to qualify for this payment, bearing in mind that app users remain anonymous."
Shadow chancellor Anneliese Dodds said Boris Johnson should use his time in isolation to fix the system.
She said: "Many people will be astonished to find that people using the COVID-19 app can't access support to self-isolate - even if they're eligible for the payment."
It comes as Downing Street announced on Sunday that England will enter a tougher three-tiered system of local coronavirus restrictions when the national lockdown ends.
The "Covid winter plan" is expected to place more areas into the higher tiers to keep the virus under control to ensure further restrictions are not needed, No 10 said.
The tiers are expected to be strengthened to safeguard the gains made during the national lockdown.
The Prime Minister is expected to say that pubs will be allowerd to close at 11pm, although last orders will be called at 10pm.
Ministers will detail what tier each area will be placed into on Thursday and MPs are expected to be given the vote to approve the new system, as promised by Mr Johnson, in the days before it comes into force on December 2.
Watch: What is Long Covid?