I stand a bit corrected regarding reply to your first question wherein it is asked if in amnesty scheme stamp duty is paid with penalty and afterwards it is found that it was deficit, can the deficit amount be recovered despite the duty having been determined by the Collector of Stamps?
I had replied it as per Indian stamp Act, 1899; for therein lies no appeal on the order of Collector once it is certified that proper stamp duty is paid; neither there is any provision for revision of collectors this order. Sec 56(1) of Indian Stamp Act only states that this power exercised by collector is subject to the control of Chief Controlling Revenue Authority. It does not say anything more. Rather it is silent on how this action is subject to the control of the Chief Controlling Revenue Authority.
Hence as per Indian stamp Act, 1899, such certificate endorsed by Collector can only be challenged on reference to High court. Civil court has no power to review the Collector's certificate.
However in Bombay Stamp Act, 1958 there is a provision for appeal on the above order of Collector. Sec 53 (1)(A) provides for this. [Sec 53 (1)(A) is inserted by way of an amendment in 1997].This section provides that any person aggrieved by Collector’s such order , may within sixty days from the receipt of such order , by an application in writing accompanied by a fee of Rs three hundred file an appeal against such order to the Chief Controlling Revenue Authority. Chief Controlling revenue authority then gives parties a reasonable opportunity of being heard and passes his order. This order is final. It can only be challenged through a writ in High Court.
Moreover, sec 53 (A) of Bombay Stamp Act provides for revision of Collectors abovesaid order. [Sec 53(A) is also inserted by way of an amendment in Bombay stamp Act in 1985]. As per sec 53 (A), The Chief Controlling Revenue Authority has power to call for the records and give parties a reasonable opportunity of being heard and then can modify the order passed by collector. This revisional power can be exercised within a period of six years from the date of certificate of the collector.
However, as per sec 53 (1) of Bombay stamp Act, if the collector’s order is regarding determining the true market value of the immovable property as described in sec 32-A (1), is non-appealable order to the Chief Controlling Authority.
Regarding whether collector of stamps can himself challenge his own order-
Neither the central act nor the state act (Bombay Stamp Act) confers such power to the collector. Appeal is always against somebody else’s order, so definitely collector can not do this himself. I think what you mean to say is whether he can review his own order. The Act says , no.. As per sec 53 (A) of Bombay Stamp Act, revisional power lies only with the Chief controlling Revenue Authority, and in certain circumstances like admissibility of instrument in evidence in courts for want of sufficient stamp duty , as per sec 58 of Bombay Stamp Act, to only such courts .
In case of doubt regarding amount of duty, collector can only refer it to the Chief Controlling Revenue Authority, as per sec 53(2) of the Bombay Stamp Act.
Note:- above applies for state of Maharashtra, I can not say for other states.