While Shettar and Rajnath Singh said the meeting here was just a "courtesy call", party insiders said the political situation in Karnataka was the main discussion point.
Addressing reporters after the meeting, both downplayed the threat faced by the state government.
"I can say with full confidence there is no crisis in Karnataka. Our government will complete its full term," Rajnath Singh told reporters.
"It was a courtesy call," he said.
Shettar echoed the new BJP president.
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"There is no crisis in Karnataka. Our MLAs have not resigned," Shettar said.
"I met him to wish him that he became (BJP's) national president," he added.
Notwithstanding their seeming confidence, the threat of a political crisis looms large in Karnataka with 13 members of the ruling BJP threatening to quit from the assembly. The 13 are loyalists of party's former leader B.S. Yeddyurappa and have been waiting since Wednesday to submit their resignation to Speaker K.G. Bopaiah.
Bopaiah, who has been out of Bangalore since late Tuesday, is expected to resume work Jan 28 or 29 when the resignations would be submitted to him.
Governor H.R. Bhardwaj had said Saturday that the Shettar-led government has a majority but he would direct the chief minister to seek a trust vote if the need arose.