The ministry also reported seven cases of BA.2.12.1 in the community, from whole genome sequencing of tests returned on May 18.
"These Omicron subvariants are prevalent overseas and have been detected at our border for many weeks," the ministry said in a statement.
"Their presence in the community is not unexpected and further cases are expected."
The health ministry said emerging data suggested BA.2.12.1 was marginally more transmissible than BA.2, the dominant subvariant currently circulating in Aotearoa New Zealand.
There was some clinical data to suggest the BA.5 and BA.4 subvariants had increased transmissibility compared to BA.2, but no data suggesting they cause more severe illness.
The vast majority of recently sequenced cases in New Zealand continue to be of the Omicron BA.2 sub-variant, with small number of cases with the BA.1 sub-variant.
Additionally, in the past week, wastewater results have detected BA.4 or BA.5 in Auckland, New Plymouth and Porirua and BA.2.12.1 in Auckland, Bay of Plenty, Palmerston North and Taupō.
"Together the community cases and wastewater results suggest that the BA.4/5 and BA.2.12.1 Omicron subvariants are circulating in parts of the community in New Zealand."
The public health settings in place already to manage other Omicron variants have been assessed as being appropriate for managing subvariants present in our community and no changes are required.
Of the 14 deaths, 13 of these had died in the past eight days, while the historical death of a case late in 2020 was also reported.
The ministry said this case had recovered at the time of death but was recently classified as having Covid-19 as a contributory cause of their death.
"This will continue to happen occasionally due to the timing of the mortality coding process, particularly in instances where deaths where Covid-19 is a contributory cause, and the death falls outside of the 28 day period of testing positive for Covid."
Two of the people's whose deaths were reported today were in their 60s, three in 70s, three in their 80s and six were aged over 90.
"This is a very sad time for whānau and friends and our thoughts and condolences are with them," the ministry said.
One person was from Northland, three were from the Auckland region, one was from Taranaki, one from Whanganui, one from the Wellington region, one from Nelson-Marlborough, four from Canterbury, one from South Canterbury and one from Southern.
"Out of respect, we will be making no further comment on these deaths."
The total number of reported deaths with Covid-19 is 1210 and the seven-day rolling average is 12.
The locations of today's community cases are Northland (161), Auckland (1907), Waikato (443), Bay of Plenty (196), Lakes (77), Hawke's Bay (189), MidCentral (227), Whanganui (73), Taranaki (177), Tairāwhiti (45), Wairarapa (55), Capital and Coast (556), Hutt Valley (237), Nelson Marlborough (239), Canterbury (1007), South Canterbury (99), Southern (467) and the West Coast (73).
Of the 390 cases in hospitals across Aotearoa, they are: Northland (4), Waitematā (41), Counties Manukau (30), Auckland (78), Waikato (25), Bay of Plenty (seven), Lakes (three), Tairāwhiti (four), Hawke's Bay (14), Taranaki (eight), MidCentral (14), Wairarapa (four), Hutt Valley (14), Capital and Coast (32), Nelson Marlborough (nine), Canterbury (59), South Canterbury (10), West Coast (one) and the Southern region (33).
The ministry said the hospitalisation figure provided today for Waitematā DHB was yesterday's number. Today's number would be updated online as soon as it came through.
Meanwhile, 69 imported cases have been detected.
There are 47,933 active community cases.
The seven-day rolling average of community case numbers today is 6850 while last Friday, it was 6960.
Health authorities have reminded people heading away over Queen's Birthday weekend to have a plan in place in case they contracted Covid-19 or were deemed a household contact.
"You would need to self-isolate and likely remain wherever you test positive or become a household contact, so there may be extra costs involved in paying for additional accommodation and changing your travel plans."
Affected people who had used their own vehicle to travel could travel back home to isolate but needed to take public health measures to ensure they did not infect anyone on their way home.
That inlcuded maintaining social distance and using self-service petrol stations.
People who used public transport or travelled between islands would not be able to isolate at their home.
"So it is important you have a plan and the ability to isolate where you are holidaying, if you need to do so."
The ministry said with all variants of Omicron, the public health advice remained the same.
"Getting your booster remains one of the best defences against Covid-19.
"Stay home if you're unwell, get tested if you're symptomatic, wash and dry your hands, cover coughs and sneezes, wear a mask in crowded or poorly ventilated indoor public settings and get vaccinated."
The usual Ministry of Health 1pm updates will be published over the long weekend on Saturday and Sunday.
However, on the public holiday, there will be no update. Tuesday's update will include the figures for Monday.
PCR testing was used to identify 214 of the new community cases reported today - while RATs were used for 6018 cases.
To date, 95.2 per cent of eligible people aged 12 and older have had two doses of Covid-19 vaccine and 72.7 per cent of people aged 18 or older have been boosted.
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Yesterday, there are 7870 new community cases of Covid-19 and a further 13-related deaths reported.
Eleven of these deaths were in the past 48 hours and two were in January this year.
Four of the people whose deaths were reported yesterday were in their 60s; one person was in their 70s; five people were in their 80s and three were aged over 90.
Four people were from the Auckland region, four were from Canterbury, two from Southern, and one each from Taranaki, Hawke's Bay, and Wellington.
The total number of reported deaths with Covid-19 is 1197 and the seven-day rolling average is 14.
One previously announced death has been removed from the ministry's totals as it was reclassified as not a Covid-19 case.
Meanwhile, there were 393 people in hospital including eight in intensive care, the ministry said yesterday.
Yesterday, it was reported there were 48,544 active community cases of the virus in New Zealand.
The seven-day rolling average of community case numbers was 6937, while last Thursday, it was 7095.
Modelling suggests a second Omicron wave could hit in the second half of this year.
It will be driven in part by people getting reinfected because their immunity has waned.
The wave is estimated to peak at fewer daily cases than the first wave, as well as fewer hospitalisations - unless infections were prevalent among higher-risk people such as the elderly.
