The Bomarc Missile Program was highly controversial in Canada.[23] The Progressive Conservative government of Prime Minister John Diefenbaker initially agreed to deploy the missiles, and shortly thereafter controversially scrapped the Avro Arrow, a supersonic manned interceptor aircraft, arguing that the missile program made the Arrow unnecessary.[23]

Initially, it was unclear whether the missiles would be equipped with nuclear warheads. By 1960 it became known that the missiles were to have a nuclear payload, and a debate ensued about whether Canada should accept nuclear weapons.[24] Ultimately, the Diefenbaker government decided that the Bomarcs should not be equipped with nuclear warheads.[25] The dispute split the Diefenbaker Cabinet, and led to the collapse of the government in 1963.[25] The Official Opposition and Liberal Party leader Lester B. Pearson originally was against nuclear missiles, but reversed his personal position and argued in favour of accepting nuclear warheads.[26] He won the 1963 election, largely on the basis of this issue, and his new Liberal government proceeded to accept nuclear-armed Bomarcs, with the first being deployed on 31 December 1963.[27] When the nuclear warheads were deployed, Pearson's wife, Maryon, resigned her honorary membership in the anti-nuclear weapons group, Voice of Women.[24]

Canadian operational deployment of the Bomarc involved the formation of two specialized Surface/Air Missile squadrons. The first to begin operations was No. 446 SAM Squadron at RCAF Station North Bay, which was the command and control center for both squadrons.[27] With construction of the compound and related facilities completed in 1961, the squadron received its Bomarcs in 1961, without nuclear warheads.[27] The squadron became fully operational from 31 December 1963, when the nuclear warheads arrived, until disbanding on 31 March 1972. All the warheads were stored separately and under control of Detachment 1 of the USAF 425th Munitions Maintenance Squadron at Stewart Air Force Base. During operational service, the Bomarcs were maintained on stand-by, on a 24-hour basis, but were never fired, although the squadron test-fired the missiles at Eglin AFB, Florida on annual winter retreats.[28]

No. 447 SAM Squadron operating out of RCAF Station La Macaza, Quebec, was activated on 15 September 1962 although warheads were not delivered until late 1963. The squadron followed the same operational procedures as No. 446, its sister squadron. With the passage of time the operational capability of the 1950s-era Bomarc system no longer met modern requirements; the Department of National Defence deemed that the Bomarc missile defense was no longer a viable system, and ordered both squadrons to be stood down in 1972.

Goose Air Base in Labrador was the site of the first US nuclear weapons in Canada, when in 1950 the United States Air Force Strategic Air Command stationed 11 model 1561 Fat Man and Mark 4 atomic bombs at the base in the summer, and flew them out in December.[18] While returning to Davis–Monthan Air Force Base with one of the bombs on board, a USAF B-50 heavy bomber encountered engine trouble, had to drop, and conventionally detonate, the bomb over the St. Lawrence river, contaminating the river with uranium-238. The detonation was near Saint-André-de-Kamouraska.[19] In 1953, Strategic Air Command constructed ten new reinforced concrete buildings as part of a heavily secured weapon storage area located at 53°17′43.9″N 60°22′36.6″W, surrounded by two barbed wire fences and several armed guard towers. Goose Air Base Weapons Storage Area was the only weapons storage area in Canada constructed to house the Mark 4, AIM-26 Falcon, and AIR-2 Genie nuclear weapons. [20]

The warheads were never in the sole possession of Canadian personnel. They were the property of the Government of the United States and were always under the direct supervision of a "Custodial Detachment" from the United States Air Force (or Army, in the case of Honest John warheads).

Through 1984, Canada would deploy four American designed nuclear weapons delivery systems accompanied by hundreds of warheads:

56 CIM-10 BOMARC surface-to-air missiles.[21]
4 MGR-1 Honest John rocket systems, each with four rockets and four warheads, for a total of 16 W31 nuclear warheads the Canadian Army deployed in Germany.[21]
108 nuclear W25 Genie rockets carried by 54 CF-101 Voodoos.[21]
estimates of 90 to 210 tactical (20–60 kiloton) nuclear warheads assigned to 6 CF-104 Starfighter squadrons (about 90 aircraft) based with NATO in Europe (there is a lack of open sources detailing exactly how many warheads were deployed).[22]

In practice, each of 36 NATO squadrons (initially six Canadian squadrons Number 1 Air Division RCAF) would provide two aircraft and pilots to a Quick Reaction Alert facility. The 'Q' aircraft could be launched with an armed US nuclear weapon within 15 minutes of receiving the 'go' order. This arrangement was called the NATO Quick Reaction Alert Force. It provided a dispersed force upwards of 100 strike aircraft for use on short notice. Missions were targeted at troop concentrations, airfields, bridges, assembly and choke points and other tactical targets in order to slow the massive tank formations of the Red Army as they poured into the Fulda Gap and on towards the Rhine River.

In total, there were between 250 and 450 nuclear warheads on Canadian bases between 1963 and 1972. There were at most 108 Genie missiles armed with 1.5 kiloton W25 warheads present from 1963 to 1984. There may have been fewer due to attrition of CF-101s as the program aged and as incoming CF-18s became combat-qualified.[23] In addition, between 1968 and 1994 the United States stored the Mk 101 Lulu and B57 nuclear bombs at Naval Station Argentia, Newfoundland.[24]

This number decreased significantly through the years as various systems were withdrawn from service. The Honest John was retired by the Canadian Army in 1970. The Bomarc missile was phased out in 1972 and the CF-104 Strike/Attack squadrons in West Germany were reduced in number and reassigned to conventional ground attack at about the same time. From late in 1972, the CF-101 interceptor force remained as the only nuclear-armed system in Canadian use until it was replaced by the CF-18 in 1984.[25]