The Perth-based utility, which supplies around nine million customers, blamed "very competitive market conditions" for a drop in electricity and gas customer accounts from 9.10 million to 8.99 million by the end of June.
The business, which trades as Southern Electric, Swalec and Scottish Hydro, also saw gas usage plunge 29% and electricity fall 7% due to milder weather.
SSE, along with the other big energy providers, has come under fire for raising prices and now faces a Competition and Markets Authority (CMA) probe to see if there is enough competition in the UK energy market.
The CMA is expected to publish its provisional findings in May or June next year.
SSE, which held its annual meeting today, said the investigation was an "important opportunity to demonstrate the competitiveness of the energy market in Great Britain."
SSE loss of customers in the first quarter of its financial year comes after the business lost 370,000 customer accounts in the year to March.
This prompted SSE to freeze prices in March until January 2016, after putting up gas and electricity bills by 8.2% last October.
But the business, which plans to cut 500 jobs, said its financial performance was on track as it looks to boost its dividend at a rate that at least keeps pace with the retail price index (RPI) measure of inflation for 2014-15. RPI inflation stands at 2.6%.
The business said it was in the middle of selling PFI street-lighting contracts and non-regulated gas pipelines, which it is confident will complete by the autumn.
SSE has set out plans to spend £5.5 billion on investment in the four years to March 2018, including £1.6 billion in the current financial year.
Last week the group was granted planning permission to build a £1.2 billion undersea electricity cable linking green energy projects between Caithness and Moray in Scotland.