The CDs had data on the 30,000-plus who were employed by Glasgow City Council in 2007 and the 20,000-plus still employed in 2009 after the authority transferred thousands of staff to its arms-length companies.
The CDs were given to Edinburgh-based solicitors Fox and Partners, which is involved in a massive equal pay case against the council. But when the legal firm sent them to a third party for analysis, only an empty envelope arrived.
Sources insist the CDs were encrypted when they were dispatched by courier from the city council to the legal firm, with the password sent electronically. However, it is unknown if the data was still secured when the discs went missing.
The Herald understands the CDs contained payroll numbers, gender, job description and title but not names or bank details.
The source said: "We were compelled to share some information, general payroll data. It was essentially everyone who worked for the council in 2007 and again in 2009, when it would have been less due to the creation of the Aleos (arm's-length external organisations).
"We gave it to Fox and Partners fully encrypted and sent it by courier. The password was sent electronically. Thereafter we don't really know, apart from it was sent to a third party and didn't arrive, only an envelope did and the police are now investigating."
It is the latest of several incidents where information held by the council has gone missing.
Last year a laptop containing unencrypted details of thousands of city residents and businesses was stolen from an office in the City Chambers, leading to claims that scores of other laptops were unaccounted for.
The latest loss came to light after members of the city council's Green Party group were given some of the details.
Councillor Martha Wardrop then raised the matter at a finance committee. She said: "Officers said they were aware of it and that it was being investigated. We were also given an update on the actions taken since the breaches of data protection last year.
"But this raises another issue, relating to what safety measures second and even third parties we are involved with have in place. It's something we need clarity on and I will be asking for those assurances."
Last night Carol Fox, of Fox and Partners, said she could not discuss the missing data due to the ongoing equal pay tribunal.
She added: "I can't really comment. We are in the middle of a tribunal and this is part and parcel of proceedings."
A city council spokesman said: "We were obliged to provide information, which we did in a secure and anonymised format. This was subsequently lost by a third party. While any data loss is regrettable, we are confident there is no risk to our staff."