The funding, announced yesterday, was the eighth round of government funding.
Central Otago Clutha Trails Ltd, which operates the Roxburgh Gorge Trail and Clutha Gold Trail, received $82,721, the most in Otago.
About $63,000 of the funds was for run-off and water-table improvements to better manage heavy rainfall and reduce maintenance costs.
Nearly $20,000 was for trail repairs following the flash flooding in Roxburgh on November 26 last year.
Central Otago Clutha Trails co-director Murray Paterson said the maintenance funding would help future-proof the trails.
"It certainly is helpful and it helps us keep the trail up to the standard we want it, in top condition.
"We're getting more riders on it all the time and getting a lot of good reports from it but we just want to make it better all the time."
The Queenstown Trail received $15,125 to build 600m of off-road trail to replace the route from the busy Lower Shotover and Domain Rds.
The Alps 2 Ocean cycle trail received $14,203 to repair flood damage to the Kurow-to-Oamaru section caused by heavy rainfall during Cyclone Gita.
Trails around New Zealand received $820,510 in total.
The largest amount - $300,000 - went to Tasman's Great Taste Trail, in the Nelson-Tasman region, for recovery works following storms in November and February.
Tourism Minister Kelvin Davis said the Government wanted to ensure the cycle trails were well looked after.
"The cycle trails are tools for regional development, helping attract visitors year-round and providing opportunities for local businesses to sprout up or expand."
