HM Revenue and Customs (HMRC) officials were warned to ensure CDs containing benefit details of 25 million people were delivered "as safely as possible".
Police are continuing to search for the discs at HMRC offices
The warning from a National Audit Office (NAO) official was sent 16 days before the information went missing.
It is one of a string of e-mails released by ministers as they seek to prove top officials did not sanction the sending of sensitive data.
Another e-mail reveals concerns about the cost of removing bank details.
The government has been under fire since it was revealed the two discs went missing after they had been sent by unregistered internal post.
The Conservatives say the crisis is down to "systemic" errors at HMRC - but the government insists it was the fault of low level civil servants.
Ministers released the e-mail exchanges, from March and October this year, in a bid to prove their case.
One of them was sent by an NAO official on 2 October, 16 days before the data went missing. It said: "Please could you ensure that the CDs are delivered to NAO as safely as possible due to their content."
The same e-mail also asked the recipient to ring the NAO when the CDs had been received so that the relevant passwords could be passed on.
Another message, dated 13 March from an NAO official, with all names blanked out, says: "I do not need the address, bank or parent details in this download - are these removable to make the file smaller?"
The e-mail is marked: "URGENT Extract from Compliance scan," its importance is listed as "high" and its sensitivity "confidential".
But another e-mail from the same day, from an HMRC official, appears to suggest officials were concerned about the cost implications of stripping sensitive data from the files.
It says: "I must stress we must make use of data we hold and not over burden the business by asking them to run additional data scans/filters that may incur a cost to the department".
But the HMRC has stressed that although one of its senior officials was copied in to the e-mail exchanges from 13 March, there is no evidence that he or she made the decision to release the data.
Caroline Mawhood, the NAO's assistant auditor general at the NAO, says in a covering letter to HMRC Acting Chairman Dave Hartnett: "The email was sent by a junior HMRC manager. It refers to a reluctance to provide data in the filtered form the NAO had requested.
"We also agreed that our own NAO audit director was aware of this position, and that we have no evidence that the Process Owner for Child Benefit made the decision to release the data. The NAO is not making any issue of this."
A National Audit Office letter also reveals Child Benefit files were sent to accountancy firm KPMG. The firm says the files were returned "by hand" to the NAO and that any information on its own system has been deleted.
Shadow Chancellor George Osborne said far from clearing senior officials of blame the e-mails released by the government were evidence of "systemic failure" at the HMRC.
MISSING DATA INCLUDES
National insurance number
Name, address and birth date
Names, sex and age of children
Bank/savings account details
He said Chancellor Alistair Darling now faced "serious questions about the version of events he gave earlier this week that this was some lone figure sitting by themselves at a computer. That is not what these e-mails reveal".
In a separate development, the government is seeking to reassure people that their personal details have not fallen into criminal hands.
In a letter being sent to seven million families, HMRC apologises for losing the data but says it is still "likely to still be on government property".
It says police are continuing to search for the discs but "there is no evidence that it is in the possession of anyone else".
The Metropolitan Police refused to comment on the claim that the discs were probably still on government property.
A Met spokesman said they were continuing to search the HMRC's offices in Tyne and Wear and the NAO offices in London.
On Wednesday, Prime Minister Gordon Brown apologised for the data loss but said it was down to officials not following the rules rather than "systemic" failures at HMRC caused by budget cuts.
He has ordered security checks on all government departments to ensure data is properly protected.
HMRC is protecting the identity of the official blamed for sending the two discs containing the details of 25m people by courier from the Child Benefit office in Washington, Tyne and Wear, to the NAO in London on 18 October.
The official, who the BBC understands is a 23-year-old man, has reportedly been suspended pending disciplinary action.
Two further discs, containing National Insurance numbers, but not bank details, are also reported to have gone missing from HMRC's offices.
Her Majesty's Revenue and Customs has set up a Child Benefit Helpline on 0845 302 1444 for customers who want more details.
LOST CDS - SEQUENCE OF EVENTS
18 October - Junior official from HMRC in Washington, Tyne and Wear, sends two CDs containing password-protected records to audit office in London through courier TNT, neither recorded nor registered
24 October - When package fails to arrive, second one is sent by registered post and arrives safely
3 November - Senior managers are told first package has been lost
10 November - Prime minister and other ministers are informed
12 November - HMRC tell ministers CDs will probably be found
14 November - When HMRC searches fail, Metropolitan Police are called in
15 November- Richard Thomas, Information Commissioner, says remedial action must be taken before public is informed
20 November - HMRC Chairman Paul Gray resigns; Chancellor Alistair Darling makes announcement to House of Commons
21 November - Prime Minister Gordon Brown apologises and orders security checks