Whenever the taxpayer is considered delinguent or there is a tax deficiency, the taxpayer is subjected to a 25% civil penalty or surcharge on the amount of tax due. Should there be willful neglect to file a return or a false or fraudulent return is willfully made, then the civil penalty or surcharge is 50%. 
Provided that failure to report sales, receipts of income in an amount exceeding 30% or a claim of deductions in an amount exceeding 30% of actual deductions shall constitute prima facie evidence of a false or fraudulent return. (Sec. 248, NIRC).

Also, any unpaid amount of tax shall be assessed and collected a 20% per annum interest from the date prescribed for payment until the amount is fully paid (Sec. 249, NIRC)

A specific taxpayer/s is subject of a request for the supply of tax information a foreign tax authority pursuant to an international convention or agreement on tax matters to which the Philippines is a signatory or a party of, provided that the requesting foreign tax authority is able to demonstrate the foreseeable relevance of certain information required to be given to the request (Sec., 3 & 8, RA10021).

A protested or disputed assessment is where a taxpayer questions an assessment, and ask the collector to reconsider or cancel the same because he believes that he is not liable therefor.

-St. Stephen's Assoc vs. CIR, GR No. L-11238

One year from the date of sales

NOTE: For purposes of reckoning the one-year period on the foreclosed assets of natural persons and the period within which to pay Capital Gains Tax or Creditable Withholding Tax and DST on the foreclosure of Real Estate Mortgage shall be reckoned from the date of registration of the sale in the Office of the Register of Deeds.

Distraint and levy may be repeated if necessary until the full amount of the tax delinguency due, including all expenses, is collected from the taxpayer (Sec 217).

Further distraint and levy is necessary so that a clever taxpayer who is able to conceal most of the valuable part of his property from the revenue officers to escape payment of his tax liability by sacrificing an insignificant portion of his holdings.

-Castro vs. CiR, No. L-12174, April 26, 1962

A claim for refund partakes the nature of an exemption which cannot be allowed unless granted in the most explicit and categorical language. Hence, before recovery is allowed, it must be established that there was an actual collection and receipts by the Government of the tax sought to be recovered and this requires factual proof.

-CIR v. S.C. Johnson and Son, GR No. 127105, June 25, 1999

There is a mistake of fact when a taxpayer erroneously pays a tax, as for instance in case where he is not aware of an existing exemption in his favor at the time the payment was made. (UST Coop Store vs. City of Manila, GR L-17133, December 31, 1965).

The proper party to question, or seek a refund of, an indirect tax is the statutory taxpayer, the person on whom the tax is imposed by law and who paid the same even if he shifts the burden thereof to another (GR 171383 & 172379, Nov. 14, 2008).

The withholding agent has a legal right to file a claim for refund. First, because he is considered a "taxpayer" under the NIRC as he is personally liable for the withholding taxes should it be found to be less than the amount that should have been withheld under the law. Second, as an agent of the taxpayer, his authority to file the necessary income tax return and to remit the tax withheld impliedly includes the authority to file a claim for refund and to bring an action for recovery of such claim (CIR vs. Smart Communications Inc., GR No. 179045-46, August 25, 2010).

While the withholding agent has the right to recover the taxes erroneously or illegally collected, he nevertheless has the obligation to remit the same to the principal taxpayer.

-2 years from payment (Sec. 229, NIRC).
The claim for refund must be filed within the 2 years from the date of payment of the tax or penalty regardless of any supervening cause.

-For INPUT VAT, 2 years from close of taxable quarter, not from the date of payment
(CIR vs. Aichi Forging Company, GR No. 184823, October 6, 2010)
(CIR vs. Mirant, GR 172129, September 12, 2008)

-For corporate taxpayers - from the filing of final adjustments returns (GR 96322. December 20, 1991)
-Other supervening events - from the date the taxpayers becomes entitled to refund. GR No. L-28467, Feb. 28, 1973
-If tax is paid by installment - from the time of final payment (GR L-11976, August 29, 1961)