Raja Rama Varma , a nephew of the previious Raja, grand son of Chittamma thampuran's daughter Subhadra, suceeded him  in 1844,   This Raja was soon developing a dislike for the extremely talented and experienced Dewan. Did this come about because of sheer jealousy and unfounded suspicions is the question.

  The Raja continued to complain in writing to the Resident, the Governor of Madras and the Court of Directors of the Company for years and finally the Court of Directors stated as follows: . “Our opinion is that under the ninth article of the treaty you are empowered to maintain in office a minister whom the Raja wishes to remove, if you have good reason to believe that the Raja’s displeasure is occasioned, as you hold to be in this case, by the honest endeavors of the Dewan to perform his duty in conformity to the views of the British Government. It cannot be expected that any minister will do his duty faithfully, if his dismissal is the consequence of adherence to it, and therefore, unless Shungra Warrier is supported against the displeasure which he has incurred, all hope of good Government for the Cochin territory must be abandoned. .. The Raja should therefore be informed that Shungra Warrier cannot be dismissed from office unless on some substantial misconduct proved against him to your satisfaction”.

The relationship continued to be bad and Sankara Variyar was ready to retire. But the Resident General Cullen did not allow him to do so.

  Before his death, the Raja made peace with the Dewan.  K.P Padmanabha Menon in his book on History of Cochin ( Kochy Rajya Charithram), page 733;  writes that the Raja carried on conversations with the Dewan about matters of Government and continued to occasionally  disagree with him on some policy matters.  The Raja told him that he had no doubt about the Dewan's skills as administrator but felt that he had the right to set policy. The Raja died in July 1851 at Thrissur.