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(3) The Collector may, suo motu or otherwise, within five years from the date of registration of any instrument of conveyance, exchange, gift, release of benami right or settlement not already referred to him under sub-section (1), call for and examine the instrument for the purpose of satisfying himself as to the correctness of the market value of the property which is the subject matter of conveyance, exchange, gift, release of benami right or settlement and the duty payable thereon and if after such examination, he has reason to believe that the market value of the property has not been truly set forth in the instrument, he may determine the market value of such property and the duty as aforesaid in accordance with the procedure provided for in sub-section (2). The difference, if any in the amount of duty, shall be payable by the person liable to pay the duty."
"10. On a perusal of the provisions of Section 47-A of the Stamp Act, as amended by the Tamil Nadu, it is manifest that these provisions empower the Registering Authority, while registering any instrument of conveyance to refer the matter to the Collector for determination of market value of the property and the proper duty payable on the instrument if the Registering Authority has reason to believe that market value of the property which is the subject-matter of such instrument has not been rightly set forth in the instrument. The object of the provision is only to neutralise the effect of under-valuation of property with a view to evading payment of stamp duty. The condition precedent for making a reference is, there must be reason for the Registering Authority to believe that the market value of the property has not been truly set forth in the document presented for registration and hence it must follow that the reasons must be recorded, however short it may be. ......."

(Emphasis Supplied) The Registering Officer has no jurisdiction to refuse registration of any document. Paragraphs 7 and 8 of the Full Bench decision reported in 2008 (1) LW 47 (G.Karmegam v. The Joint Sub Registrar) reads as follows:

"7. Registration of document is a sine qua non for referring the matter to the Collector, if the registering officer believes that the property is undervalued. No jurisdiction has been conferred on the registering officer to refuse registration, even if the document is undervalued. Besides, there is no authority for him to call upon the person concerned to pay additional stamp duty. Collector is the prescribed authority to determine the market value, after affording a reasonable opportunity of hearing the parties. The registering officer cannot make a roving enquiry to ascertain the correct market value of the property by examining the parties. However, it is expected that he has to give reasons for his conclusion for undervaluation, however short they may be. He can neither delay nor refuse registration of the instrument, merely because the document does not reflect the real market value of the property. In order to reach a conclusion, there is no bar for the registering officer to gather information from other sources, including official or public record. Valuation guidelines, prepared by the revenue officials periodically, are intended with an avowed object of assisting the registering officer to find out prima facie, whether the market value set out in the instrument has been set forth correctly.

The case reported in (2009) 5 MLJ 391 (Government of Tamil Nadu v. S.Jayalakshmi), though relates to suo motu power exercised by the Collector, the Division Bench in para 28 held as follows:

"28. A perusal of the impugned order and the counter affidavit filed by the second and third respondents wold reveal that the documents have already been registered and in pursuant to objections raised by the Local Audit in its reports 3/99 and 6/99 respectively, demand of additional stamp duty was made on the basis of the market value on the date of the registration of the sale deed. No doubt sub-section 3 of Section 47-A clothe the Collector the suo motu power within 5 years from the date of registration of the any instrument of conveyance etc., not already referred to him under sub-section (1) of Section 47-A to call for and examine the instrument for the purpose of satisfying himself as to the correctness of the market value of the property which is the subject matter of the conveyance etc., and the duty payable thereon and if after such examination, has reason to believe that the market value of the property has not been truly set forth in the instrument, he may determine the market value of the said property and the duty as aforesaid in accordance with the procedure provided for in sub-section (2) of Section 47-A of the Indian Stamp Act and the difference, if any, in the amount of duty, shall be payable by the persons liable to pay the duty. In the case on hand, a perusal of the impugned orders would reveal that the appellants herein has failed to take into consideration any material nor any material was placed before them to arrive at a conclusion that the market value of the property conveyed to the allottees under the respective deeds of sale has not been truly set forth and that no reasons have been recorded that the allottees had fraudulently evaded the payment of stamp duty."