In November 2014, Johnston came under fire for comments regarding the government owned defence building company, the Australian Submarine Corporation.

Opposition Senate Leader Penny Wong moved a motion to censure Johnston for his remarks on the ASC, as well as his handling of the ADF staff pay cut.

[11] Much of the anti-Liberal swing at the 2014 Fisher state by-election in South Australia, where Labor won the traditionally Liberal seat by just five votes from a 7.27 percent two-party swing to go from minority to majority government, was attributed to Johnston's "I wouldn't trust them to build a canoe" remark toward South Australia's Australian Submarine Corporation, occurring just several days out from the by-election.

[12][13][14] In December 2014, less than a month after his comments on the ASC were made, News Corp leaked images of receipts totalling thousands of dollars allegedly used by Senator Johnston's government-issued credit card to pay for the dinners of a number of companies vying for a contract to build the Collins-class submarine replacement project.

[16] A spokesperson for Senator Johnston responded by saying "All hospitality hosted by the Defence Minister and extended to foreign dignitaries or industry heads, including at the time of the Albany Commemoration, has been within guidelines and is consistent with previous defence ministers' practice" and that the senator's office was investigating the leaks and would not comment any further.