The meeting assumed significance as it came ahead of the June 27 Rajya Sabha polls to six seats from Tamil Nadu.
However, Natarajan told reporters that she met Karunanidhi to wish him as he turned 90 on June 3.
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To a query on Congress' stand on the Rajya Sabha polls, the Environment Minister said her party will decide on it.
DMK snapped its ties with UPA over the Sri Lankan Tamils issue in March last.
Karunanidhi had yesterday said DMK would hold consultations with other political parties over fielding a candidate for the Rajya Sabha polls.
Asked whether DMK had sought the support of CPI(M), he said, "We have not sought the support of any particular party. We will talk to all parties."
Each candidate needs 34 first preference votes to win in the polls.
DMK, which has 23 MLAs, needs the support of other parties if it seeks to field a candidate and ensure victory. Congress has five MLAs.
Ruling AIADMK, which can win at least four of the seats in view of its strength of 151 in the 234-member Assembly, has fielded five candidates.