Ms Ferrier admitted breaking self-isolation rules by travelling to Parliament after developing coronavirus symptoms and then taking a train back to Scotland having tested positive.
Scotland’s First Minister tweeted: “I’ve spoken to Margaret Ferrier and made clear my view that she should step down as an MP.
“I did so with a heavy heart – she is a friend and colleague – but her actions were dangerous & indefensible. I have no power to force an MP to resign but I hope she will do the right thing.”
Ms Ferrier, 60, has been stripped of the party whip and also referred herself to the police and parliamentary standards watchdog.
Mr Blackford told BBC Breakfast: “What Margaret has done is inexcusable and she knows that. She knows that she was in the wrong. I’ve expressed my anger.”
The SNP’s leader in Westminster added: “Margaret is going to have to reflect very carefully on the actions that she’s taken and will have to consider her position in the light of all of this.”
Pressed on whether she should resign, Mr Blackford said: “I think she will have to reflect very carefully as to whether or not she can continue as a member of parliament for her constituents.”
Asked again, he replied: “I think it’s pretty clear what I’m saying…Margaret has to do the right thing.”
Ms Sturgeon condemned the MP’s “utterly indefensible” behaviour and welcomed her having the whip suspended.
Other colleagues have also called for her to go including David Linden, the SNP MP in her neighbouring constituency Glasgow East.
Ms Ferrier said she took a test on Saturday afternoon after experiencing “mild symptoms”, before travelling by train to London on Monday having felt better.
She spoke in the coronavirus debate in the Commons on Monday and said she tested positive for Covid-19 that evening. It is unclear whether the Rutherglen and Hamilton West MP received the result before or after she spoke.
Her statement said she travelled home to Glasgow on Tuesday where she is now self-isolating.
She said: “Despite feeling well, I should have self-isolated while waiting for my test result, and I deeply regret my actions.”
Police Scotland said they were “looking into the circumstances” with the Met Police.
The Commons said that she did not inform her party whip until Wednesday afternoon and that one person was identified as a close contact and told to self-isolate.
An SNP spokeswoman insisted the party did not know until Thursday that Ms Ferrier had taken a test prior to travelling to London.
Scottish Conservative leader Douglas Ross, who resigned from Boris Johnson’s Government over Dominic Cummings’ lockdown movements, said that “the public deserve clear answers”.
The Communities Secretary Robert Jenrick told BBC Radio 4’s Today programme: “Nobody is above the law. And Margaret Ferrier has accepted that she broke the law on multiple occasions.
“That’s a serious situation. She needs to decide what she wants to do.”