Asked whether the 2G spectrum scam had affected the ties, he replied in the negative.
This is the first meeting between the two leaders after A Raja, a DMK representative in the UPA cabinet, resigned as telecom minister in the wake of the scam.
Karunanidhi, who was scheduled to meet Singh on Sunday night, could not do so as he was 'pre-occupied' in a meeting to release a volume of poems of his friend, noted Tamil lyricist Vairamuthu.
He said on Monday morning that his scheduled meeting did not take place as many speakers addressed the function.
Asked whether he was upset over the environment ministry not clearing the state government's eco-park in the city, scheduled to be inaugurated by Singh but cancelled at the last minute, Karunanidhi said, "No".
During the meeting, Karunanidhi submitted a detailed memorandum to Singh on the damage caused by the rains last month in several districts of the state.
He said he had requested the Prime Minister to quickly sanction funds for relief and rehabilitation.
Singh, who reached Chennai on Sunday night, would inaugurate the 98th edition of the Indian Science Congress at SRM University at suburban Kattankulathur.