A total of 1,929 homes were finished - down 29 per cent on 2016 - according to the latest Quarterly Housing Statistics for Scotland.
But the total number of new build homes completed across all sectors over the year ending September 2017 increased by five per cent, or 908 homes.
Communities secretary Angela Constance said the Scottish Government was still on track to meet its target of at least 50,000 affordable homes by 2021.
The five per cent increase in all new build completions included a nine per cent rise in private-led construction, totalling 1,194 homes, and a 21 per cent increase in local authority completions, accounting for 239 homes.
Opposition parties warned the number of long-term empty properties in Scotland had increased to its highest ever recorded level, from 20,328 in 2007 to 37,135 in 2017.
Ms Constance said: “Ensuring everyone has access to a safe, warm and affordable place to call home is at the heart of our ambition for a fairer Scotland. These latest figures show that we have now delivered nearly 72,500 affordable homes, which includes nearly 50,000 for social rent, since 2007.
“They also highlight that the number of social rented homes being started increased by 17 per cent in the latest year.
“We are committed to ensuring much greater progress, backing that with record levels of investment, with funding of £3 billion – the single biggest investment in, and delivery of, affordable housing since devolution. This includes more than £756 million for affordable housing in 2018-19 alone – a 28% increase on the previous year – and all councils have been given long term planning assumptions, totalling £1.75 billion to March 2021. That provides the assurance needed to deliver the homes required, and we know that many more developments and proposals are coming through as a result of that.”
Scottish Conservative housing spokesman Graham Simpson said: “Throughout their decade in government the SNP has seen empty properties soar, taking valuable properties out of use.
“At the same time, under the SNP, the affordable housing supply has stagnated.
“This is a record of complacency and inaction.
“For the thousands of people waiting for housing this latest increase in empty properties will feel particularly frustrating.
“The SNP must introduce a Help to Rebuild scheme which could bring together disparate grant schemes under one easily accessible umbrella programme.
“In addition, the SNP must enable empty business premises to be turned into affordable housing as well as help farmers convert empty buildings into housing.”
David Stewart, policy lead at the Scottish Federation of Housing Associations, said: “The figures show a marked increase in approvals for new housing association homes – up 33 per cent on the previous year. We always knew that delivering 50,000 affordable homes would be a significant challenge – but it is one that housing associations are committed to meeting in order to deliver much needed quality affordable homes.
“The increase in approvals for new housing association homes reflects the findings of research commissioned by SFHA and Shelter on Strategic Housing Investment Plans, which found that housing associations, local authorities, and their partners in the private sector are working hard to increase supply and on course to deliver 50,000 affordable homes.”