The move is due to the level of demand from farmers who applied while the scheme was open in February.
Over £1m of grant funding has been paid out to households and businesses directly affected by the flooding in Aberdeenshire since January.
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Speaking during a visit to Ballater, Mr Lochhead said: "Ballater has suffered badly as a result of the recent flooding and it's good to know that already more than £1 million of the funding provided by the Scottish Government has been paid out by the local council to households and businesses that were affected, and Aberdeenshire Council is still working its way through applications.
"And it's great news that there is now up to £2 million available in the Agricultural Floodbank Repair Grant Scheme to cover the standard costs of repairs to man-made floodbanks on farms which were affected by flooding in nine local authorities during December and early January."
(LM)
