Lee Kuan Yew
Operation Coldstore detentions

The Malayan government considered the arrests of Singapore's left-wing groups as non-negotiable for the formation of Malaysia. Tunku felt that Lee lacked the initiative to suppress "pro-communist elements" and warned that a Malay-led dictatorship would be instated to prevent a "socialist majority" in the next Malayan election. As the Malayans increased pressure on the Internal Security Council (ISC) to take action, Lee began supporting the idea of a purge in March 1962. The Malayan and Singapore special branches collaborated on an arrest list of major opposition members, though doubts arose if Lim Chin Siong and Fong Swee Suan could be classified as 'communists'. Up until the end of November 1962, the British declined to support the operation without a pretext, noting that Lim and the Barisan Sosialis had not broken any laws.

The Brunei revolt on 8 December led by A. M. Azahari provided a "heaven-sent opportunity" to take action, as Lim had met Azahari on 3 December. The Malayan government convened the ISC to discuss the operation, while Singapore's Special Branch produced alleged evidence of the communist control of Barisan. On 13 December, Lord Selkirk gave his authorisation for the arrests to proceed on 16 December. However, Lee's attempt to add two Malayan parliamentarians opposed to the formation of Malaysia into the arrest list caused the Malayan representative to rescind his consent, stopping the operation. Tunku suspected that Lee was trying to eliminate his entire opposition, while Lee felt that Tunku was evading his shared responsibility for the arrests.

An ISC meeting was scheduled to be held on 1 February 1963 to remount the operation. During the interim period, Lee had added three names from the United People's Party, one of them being former PAP minister Ong Eng Guan. Selkirk expressed concerns that Ong's arrest lacked any justification and Lee conceded that it was meant as a "warning" to Ong. Tunku told Geofroy Tory, the British High Commissioner in Kuala Lumpur on 30 January, that 'if this operation failed, merger with Singapore was off'. Selkirk was pressured to put his reservations aside and finally consented. On 2 February, Operation Coldstore commenced across Singapore, with 113 detained including Lim and 23 others from Barisan Sosialis. Lee offered Lim a path into exile which Lim rejected. The Malayans and British later pressured Lee to retract his comment when he said he "disapproved" of the operation.

In his memoirs, Lee portrayed himself as reluctant in supporting the operation, though declassified British documents revealed that Lee was "somewhat more enthusiastic" than he eventually admitted.
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