The Scottish Conservatives insisted the phones should now be withdrawn amid concerns some are being used to deal drugs.
A Freedom of Information response from the Scottish Prison Service showed mobile phones have been temporarily seized 1,899 times since May 2020.
The highest number of confiscations was in Glasgow's HMP Barlinnie, with 342, followed by HMP Edinburgh with 262.
Around 7,600 mobile phones were provided to prisoners at the start of the Covid lockdown at a cost of £2.7 million.
They were supposedly tamper-proof but some were reportedly hacked "within hours" and used for criminal activity.
The Tories said the punishment for misusing a prison-issued phone is a one-month confiscation – after which it can be returned following a review.
The party's community safety spokesman Russell Findlay said: “This scheme was introduced in good faith at the start of lockdown but it has become a farce.
"These supposedly un-hackable handsets were compromised almost immediately yet this was kept secret from the public and MSPs.
"It is absolutely right that prisoners should have access to their families, but this ill-conceived scheme has backfired badly."
He added: "They must be withdrawn immediately and permanently, and any replacement must be safe and secure."
A spokesman for the Scottish Prison Service said the phones had allowed prisoners to stay in contact with family during the pandemic.
He said thousands of calls had also been made to the Samaritans from prisoners seeking help.
The spokesman said the vast majority of the phones are used as intended.
A Scottish Government spokesman said: “While primarily an operational matter for the prison service, the provision of mobile phones, in the absence of in-person contact over sustained periods of time, has been vital in addressing the negative impacts of Covid-19 in our prisons – for staff, prisoners and families impacted by imprisonment.
“The vast majority of phones issued have been used as intended and – as these figures clearly show – where any breach of the rules takes place this is treated seriously by the prison service.”