The MP for Rutherglen and Hamilton West was suspended by the SNP following her 800 mile trip to Westminster while being infected with Covid-19.
However she remains a member of the party with Nicola Sturgeon coming under pressure to expel the MP.
Ms Ferrier told the Scottish Sun that her apology had not been written by her, and that the SNP had told her she would be allowed to return to the party because she was co-operating.
She added that she believed the whip was only withdrawn after the SNP leadership including Westminster leader Ian Blackford and Ms Sturgeon saw the response from the public.
However, Ms Sturgeon rejected the accusation during her daily coronavirus briefing and repeated her call for Ms Ferrier to quit as an MP.
When asked why the SNP waited more than an hour to withdraw the whip and for her to condemn the actions of her MP, the First Minister blamed the delay on Mr Blackford losing phone signal while on the train.
She added that there was “no great mystery” to the delay and said her own delayed response was due to being involved in other commitments and only accessing Twitter late in the day, rather than waiting for the public response to the story.
Ms Sturgeon said: "I tweeted that night and to be perfectly blunt about it I tweeted it as soon as I was able to get on Twitter.
"I do have other things that I have to do on a daily basis that means I don’t sit on Twitter literally every minute of every day.
"Ian Blackford spoke to Margaret Ferrier about the removal of the whip and as I explained at the time, Ian was travelling from London back to Skye at the time.
"Certainly when I was speaking to Ian that evening he was going in and out of mobile phone reception because he was travelling through the Highlands so again there’s no great mystery there."
When asked about the apology being drafted by the SNP and not Ms Ferrier, Ms Sturgeon said that fact should not be a “surprise” to anybody.
She added: "I don’t think it would surprise journalists or anybody else that in a situation like this somebody in her position would be assisted in putting together the actual statement that they were issuing but equally it shouldn’t surprise anybody that they were given some time in order to alert anybody that they wanted to alert.
"I know there is always a tendency to look for the intrigue behind these things but sometimes it is just more boring than that and it is just the logistics and the practicalities that have to be gone through.
"We have been pretty clear, pretty robust, and pretty tough, I am sure there will be suggestions from some people that we’ve been too tough on Margaret but in my estimation right now, knowing how important it is for me to be able to encourage other people to do the right things, we can’t turn a blind eye when somebody acts in such flagrant breach.”