The loan was to provide extra infrastructure for a second stage of 10,000ha, in addition to the 10,000ha in the first stage.
The company has repaid almost $1 million and the loan, with accrued interest, now sits at $12.272 million.
The payment was made by company chief executive Robyn Wells at the public forum before last Wednesday's council meeting and comprises principal and portions of interest on 356 shares recently issued, representing 356ha of further irrigation, after two initiatives completed this year.
One was the Duntroon extension line along Smillies Rd and into Kokoamo, resulting in an extra 288ha of irrigation.
The second was 68 shares from consolidating some resource consents for water from the Waiareka Creek under a single management group with the goal of providing co-ordinated, efficient and stable management of creek flows.
Any growth of the scheme needed to be accompanied by best management practices that included good environmental standards and processes to provide a reliable and durable solution to water issues of the past, she said.
The company was assessing several options for the stage 2 expansion and would be looking for feedback from the community as it made decisions on the design and layout.
Company chairman Alan McLay said it was gratifying to make the repayment, adding to the $500,000 it repaid last year.
"It represents that the faith the community put in us in granting the initial loan was not misplaced," he said.
The company would add incrementally to the scheme in the coming year while finalising feasibility studies towards stage 2.
