Ms Zaghari-Ratcliffe completed a five-year sentence earlier this month in Tehran on spying charges levied by Iranian authorities, the last year of which was spent under house arrest.
“The best thing to help cases such as these is to avoid politicising them,” the Iranian foreign ministry spokesman Saeed Khatibzadeh told a news conference on Monday.
He added: “I advise the British government to allow this case to go through its judicial process.”
On Sunday foreign secretary Dominic Raab condemned the decision to pursue a second case against Ms Zaghari-Ratcliffe – accusing the Iranian government of putting her “through a cruel and disgraceful ordeal”.
Ms Zaghari-Ratcliffe, arrested in April 2016, is a project manager with the Thomson Reuters Foundation, a charity that operates independently of media firm Thomson Reuters and its news subsidiary Reuters.
Antonio Zappulla, chief executive of the Thomson Reuters Foundation, said the second trial was a deliberate move to prolong her ordeal and her suffering.
Her husband Richard Ratcliffe said his wife’s future was still uncertain, facing open-ended detention, but that she was “relieved” it appeared to be her last trial.
“I think the judge saying this is the last trial is just a nice feeling – I think it is a bit like you’ve done an exam, it was horrible, you don’t know whether you passed or not, but at least it is done and there’s just a relief that comes with that.”
Mr Ratcliffe said he was feeling “better than I was expecting” but was still “cautious and worried”, adding: “I thought there was every chance that they would drag this out over a number of court cases.”
He added that he expected his wife to be convicted in the next week, but did not know what sentence she would receive.
Some observers have linked Ms Zaghari-Ratcliffe’s case to a long-standing debt Iran alleges it is owed by the UK.
Iranian media reported that during a call with Mr Johnson last Wednesday, Iranian president Hassan Rouhani raised the issue of ahistorical debt of £400m.
Tehran claims Britain owes the Islamic Republic in capital and interest for a 1970s’ arms deal with the then-Shah of Iran.