I think it is important to get some of the facts straight.
It is necessary to stress that there was no direct popular vote. Elections were held in 1964 for ‘Basic Democrats’ - effectively Union Councillors. These were elected in the main by popular vote, but the allotment for FATA - representing 9% of the total number of Basic Democrats - came from direct appointments rather than elections. The total number of Basic Democrats amounted to 80,000 and they collectively formed the electoral college for the Presidential election in 1965. It was therefore an indirect vote.
As the Basic Democrats owed their existence to Ayub and as voting for Fatima Jinnah could have risked voting in an entirely new system which either dispensed with the Basic Democrats or clipped their power, it is not surprising that they opted in the majority for Ayub. Ayub could also use the machinery of government and state media to his benefit. It has also been suggested that pressure was put on Basic Democrats, through either intimidation or bribery to vote for Ayub.
In the end, Ayub registered 49,951 of the votes to Fatima Jinnah’s 28,691. Ayub did better in West Pakistan, taking 73.6% of the vote, but he also prevailed in East Pakistan - obtaining 53.1% of the vote.
Fatima Jinnah was able to win in three major urban centres - Karachi, Dhaka and Chittagong. In the case of East Pakistan, Ayub did better in the less developed northern districts and tended to be supported by refugees in Khulna and Rajshahi Divisions who were less supportive of East Pakistani separatism.
This was in contrast to Karachi (where Fatima Jinnah got 1,061 of the votes to Ayub’s 907). Fatima Jinnah’s core constituency was amongst the refugees, who had become disillusioned by the establishment over the years. She was helped by the support of Jamaat-e-Islami (JI), despite its less than enlightened view of leadership by women. Before the rise of the MQM, the JI was influential amongst the refugees of Karachi.
To digress, in the 1950s, the social work of the JI included: clearing waste in refugee camps, burying unclaimed corpses, and providing food to the poor. It also provided medical help through the operation of a number of mobile and permanent dispensaries. By 1958, it was running more than fifty permanent dispensaries and over one hundred medical centres in Karachi. When refugee areas were destroyed by fire in 1958, it was JI workers who were first on the scene. In short: in the early years the JI was very active in providing welfare assistance in a context where the state’s policies in rehabilitating refugees in Karachi were perceived to be dilatory.
Following the Presidential Election in January 1965, National Assembly elections were held in March, with the Basic Democrats again forming the electoral college. Ayub’s party obtained 49.6% of the popular vote in East Pakistan and 61.3% in West Pakistan.
The British High Commission, in May 1965, reported to the British Secretary of State for Commonwealth Relations that, “As in the Presidential election,” in the National and Provincial elections:
“strong pressures had been applied to the electors before they entered the polling booths. In West Pakistan the police and the district administration were assiduous in urging the B.Ds. [Basic Democrats] to vote for the P.M.L. [Ayub’s party] candidates. Bribery was widely, if not universally employed – the price of a vote was quoted at Rs.3,000, and one successful candidate was said to have spent 45,000 [British Pounds] on bribes and treating. (One wonders what he expects to get on his investment.) It is significant that the only opposition success in West Pakistan was in a Karachi seat where a family quarrel rendered the P.M.L. candidate unable to pay the sums he had promised, whereat [sic] the outraged electors returned his astonished rival.”