Bereaved families could face delays in arranging cremations while filters are installed to lower pollution.
Filters which will cut mercury emissions from tooth fillings by up to 99% are being installed in Gwent, Margam and Bangor crematoria.
Gwent said it will only have half of its usual 15 services a day until March as it strives to meet the UK government target of 50% mercury reduction.
Funeral directors have warned of delays of up to a month.
But they say they are working with neighbouring crematoria to try to ensure families are not kept waiting too long during a "difficult and distressing time".
Strict rules for crematoria to limit mercury pollution with special equipment by 2012 were announced in 2005.
Exposure to the metal is linked to damage to the brain, nervous system and fertility with crematoria responsible for around 16% of the UK's mercury pollution.
Swansea and Thornhill in Cardiff, have already fitted the filters.
'Busier winter months'
Gwent Crematorium in Croesyceiliog is the only crematorium in the Torfaen, Newport, Blaenau Gwent and Monmouthshire area and carries out an average of 2,750 cremations a year.
Work to fit its mercury filters and construct a building to house them will go on until March.
The crematorium will hold services until 1pm, with building work taking place in the afternoon.
Newport city council, which has legal responsibility for the crematorium, apologised for the inconvenience.
"We need to meet Environment Agency targets relating to mercury emission, and work is needed to be carried out to ensure we comply with the new legislation aimed at limiting mercury pollution," said a council spokesperson.
"We will still be able to do up to eight services a day and while demand for cremations may increase later in the year, we will do our utmost to ensure families can choose to have a funeral on a date they choose and that any disruption is kept to a minimum."
Newport funeral director Michael Ryan said some funerals had already been delayed by two weeks, and he estimated there could be waits of a month or more in winter.
"In fairness to Gwent Crematorium, we've known about this for six to eight months and I've put in place plans to try to ensure a family doesn't want to wait very long for a cremation.
"For example, Thornhill Crematorium has been very supportive and will do the back up if they can. There's also Glyntaff Crematorium in Pontypridd which we could use.
"It's a distressing time and it may cause further distress but so far families have been understanding."
Mr Ryan said that so far his company was paying for the extra petrol costs if they needed to use another crematorium.
Similar work at Margam Crematorium in Neath Port Talbot is starting next weekend.
Deputy superintendent Malcolm Gosby said he hoped there would be minimal disruption at Margam which holds has an average of 1,300 cremations a year.
"We're doing the work in various stages and it should take about three months as we don't have to build a separate building," he said
"We will have to take it on a case by case basis but we are aiming to keep disruption to a minimum and funeral directors will be able to help families if they need to find another crematorium."
New filters are also being installed Bangor Crematorium, where about 1,000 cremations take place every year.
Llwydcoed Crematorium in Aberdare is also preparing to fit the equipment soon, Rhondda Cynon Taf council said.
Some crematoria which are unable to install the large filters - because of cost or lack of space - have instead opted to join a "burden-sharing scheme" from January 2013.
This system of buying credits allows them to continue high emissions of mercury if they are balanced by cuts at other crematoria which have installed the equipment.
Rick Powell, secretary and executive officer of the Federation of Burial and Cremation Authorities, said that of around 490,000 deaths each year in England and Wales, just over three-quarters were followed by cremation.
He said moves to comply with legislation on mercury emissions were progressing well.
"We've been dealing with this since 2005 - the sector has responded extremely positively," he said.