From Pirate Wiki
Unique Identifiers on ballots violate Human Rights
Each ballot in any New Zealand election (local and general) has a unique identifier that can later be connected with a particular voter. This practice conflicts with human rights.
Artikel 21 of the Universal Declaration of Human Rights states: 
(3) The will of the people shall be the basis of the authority of government; this will shall be expressed in periodic and genuine elections which shall be by universal and equal suffrage and shall be held by secret vote or by equivalent free voting procedures.
The OSCE Election Observation Handbook - Fifth Edition (2005) states in chapter 3.5 on page 23 about the practical implications of applied human rights: "Voters should mark their ballots ... in such a way that the marked ballot ... cannot be later connected with a particular voter." 
It could be argued that New Zealand is not a member of the OSCE but the OSCE commitments are directly derived from the UDHR and New Zealand has also ratified other treaties with similar implications.
For example have the rights included in the UDHR been reiterated and expanded in the International Covenant on Civil and Political Rights (ICCPR), an UN human rights treaty that was ratified by New Zealand. As a treaty, the ICCPR creates legal obligations for states to comply with its provisions. Article 25 of the ICCPR grants every citizen the right to vote by secret ballot. 
"Article 25 Every citizen shall have the right and the opportunity ... (b) To vote ... at genuine periodic elections which ... shall be held by secret ballot, guaranteeing the free expression of the will of the electors;"
While New Zealand has not incorporated the ICCPR into law, it took measures to give effect to many of the rights contained within it by passing the New Zealand Bill of Rights Act in 1990. The right to vote in elections by secret ballot can be found in Section 12(a) under Democratic and civil rights: 
"12 Electoral rights Every New Zealand citizen who is of or over the age of 18 years — (a) has the right to vote in genuine periodic elections of members of the House of Representatives, which elections shall be by equal suffrage and by secret ballot;"
Official reactions to Human Rights concerns
The Minister for Local Government doesn't agree with these concerns:
The imposed penalties for electoral offences committed by voters are not enough and there have to be unique identifiers on ballots to prevent fraud but the penalties provided for offences made by electoral officers or other election officials are somehow sufficient?! 
Unlike statet New Zealand hasn't maintained it's position as one of the least corrupt countries in the world because Transparency International's Corruption Perception Index is only about perception and not factual corruption. 
Neither the Minister of Local Government nor the Department of Internal affairs hold information about the hardware used by the electoral officers, or who operates and maintains the machines used to process ballot papers. 
The Justice and Electoral Select Committee completely suppresses our Human Rights concerns!
The Pirate Party New Zealand made a submission to the Justice and Electoral Select Committee on January 31st, 2011. 
Chester Boroughs from the Justice and Electoral Select Committee doesn't "think that a court can instruct the New Zealand Parliament, a New Zealand court can instruct parliament, or any court can instruct parliament to take ... action." (Transcript of oral submission to be inserted here.)
The Justice and Electoral Select Committee has reported back it's inquiry into the 2010 local body elections.