Sajid Javid’s comments came after Prime Minister Boris Johnson announced plans to lift all restrictions in England.
Mr Johnson announced that those in England who test positive for the coronavirus will no longer be required by law to self-isolate from Thursday.
The prime minister also confirmed that free universal testing will end in April, in line with his plan to “live with Covid”.
First Minister Nicola Sturgeon said Scotland will need clarity on funding for Covid testing from the UK Treasury as it is expected to comply with all Covid testing and isolation rules.
The Covid strategy for Scotland will be announced at Holyrood on Tuesday.
However, Mr Javid told BBC Radio 4 on Tuesday morning: “If Scotland decides now to go the other way when it comes to testing, it is certainly a decision for Scotland.
“Health is a delegated matter. They will pay for it in the same way as we pay for decisions in England.
Mr Javid said that because of the new health and welfare tax: “Scotland should get hundreds and millions of extra funds from this.”
However, Ms Sturgeon said it is the UK Treasury that makes Covid funding decisions.
Covid Scotland: Nicola Sturgeon called for Scotland to be returned to ‘as close to normal as possible…
Speaking on Tuesday, Ms Sturgeon said it would be “unacceptable” for Covid funding for Scotland and other devolved countries to be “limited” based on the Covid decisions made by Boris Johnson for England.
The UK Health Secretary called the decision to lift all restrictions for England “balanced and proportionate”.
Ms Sturgeon will lay out Scotland’s strategic framework to combat Covid on Tuesday afternoon.
Ms Sturgeon said: “There will be a lot of optimism about what I will lay out tomorrow, but I have to be frank with people, we are still in a pandemic of this virus.
“We know from past experience that, for example, new options may emerge and cause new problems.
“So we need to be vigilant about that and we need to be prepared for that, but we also need to manage this risk in a much less restrictive and more sustainable way going forward so that we can all get back to normal, keep that sense of normality, even if we keep this sense of vigilance.”