At the 1962 Northern Ireland general election, Long was elected MP for Ards. Soon after his election, he made headlines by accusing the management of the Harland and Wolffshipyard of introducing "capital punishment" by sacking 2,000 men during a strike. Long initially focussed on representing the fishing industry in his constituency, and when Terence O'Neill became Prime Minister in 1964, he appointed Long as Parliamentary Secretary in the Ministry of Agriculture, with special responsibility for fisheries. Long proved loyal to O'Neill and was rewarded in 1966 with promotion to Minister for Education. Long aimed to integrate Roman Catholic schools into the state school system, which overwhelmingly took pupils from Protestant families. He negotiated a small role for the state in Catholic school governance in exchange for increasing state funding for those schools to cover all their costs. When in October 1968 students linked to the socialist group People's Democracy organised a sit-in, Long joined them but asked them to go home. He refused to sign their petition and was not able to convince them to leave.
In December 1968, Long was promoted to Minister of Home Affairs. Initially, he was minded to move to repeal legislation permitting detention without trial. Two weeks after his appointment, People's Democracy activists launched their Belfast-to-Derry march, calling for electoral and legal reform, action to reduce unemployment and to provide decent homes. Long met with Ian Paisley and Ronald Bunting, who called on him to ban the march. Long refused to so, and the march set off. It was attacked by loyalists on several occasions, finally at Burntollet Bridge where there were numerous injuries. Long claimed that Paisley and Bunting had not "threatened or hinted that their followers would cause any trouble in Derry", and claimed that Paisley's supporters had not participated in the violence. The Belfast Telegraph disputed this, and claimed that Long was being partisan. The following week, People's Democracy organised a march in Newry. It was again surrounded by violence, and several police officers were injured. O'Neill claimed that this showed that People's Democracy was not a non-violent organisation. He responded to this by introducing a new Public Order Bill, which amended the Public Order Act 1951 and among other measures made it an offence to knowingly take part in an illegal procession or meeting.
Later political career
After only three months as Minister of Home Affairs, in March 1969, Long moved to become Minister of Development. He was appointed to a four-person cabinet Security Committee which, in April, decided to request British troops to maintain order. Long loyally supported O'Neill, and when he resigned in May, many people expected Long to lose his cabinet role. Instead, new Prime Minister James Chichester-Clark moved Long back to the Minister of Education post. In August 1969, Long had a 95-minute meeting with Paisley. Paisley had a list of demands to which Long listened patiently but did not act upon. He attended the funerals of some members of the Royal Ulster Constabulary and British Army who were killed in The Troubles, and placed more welfare officers in inner city schools after claiming that riots were poisoning children's minds. Long remained in post under Brian Faulkner, despite speculation that he might resign in protest at increased use of internment. When British Prime Minister Edward Heath imposed direct rule, Long protested that this was merely a political gambit, in exchange for Labour Party leaderHarold Wilson softening his party's opposition to Britain joining the Common Market. He opposed Willie Whitelaw's reduced use of internment, claiming that "there is no doubt units of the IRA that have been broken down by internment have been able to become active again". Long was also President of the Yorkshire Association for a British Ulster; in April 1974, a member was charged with gun running to violent loyalists, a group which Long had described as "the very antithesis of Loyalism".