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* '''Increased complexity''' – While complexity of equipment is a necessary part of technological advancement, the increased complexity of the AMS milking unit over conventional systems, increases the reliance on manufacturer maintenance services and possibly increasing operating costs. The farmer is exposed in the event of total system failure, relying on prompt response from the service provider. In practice AMS systems have proved robust and manufacturers provide good service networks. Because all milking cows have to visit the AMS voluntarily, the system requires a high quality of management. The system also involves a central place for the computer in the daily working routines.
* '''Difficult to apply in pasture systems''' – as a continuous animal is pediment for an optimal utilization of the AMS unit, AMS works at their best in zero-grazing systems, in which the cow is housed indoors for most of the lactation period. Zero-grazing suits areas (e.g. the Netherlands) where land is at a premium, as maximum land can be devoted to feed production which is then collected by the farmer and brought to the animals in the barn. In pasture systems, cows graze in fields and are required to walk to the milking parlour. It has been found that it can be challenging to make cows maintain a high milking frequency if the distance to walk between pasture and milking unit is too great. Maintaining production on pasture has, however, been shown to be possible in amongst others the [http://autograssmilk.dk/ AUTOGRASSMILK] project.<ref>{{Cite web|url=http://autograssmilk.dk/results/|title=Results and deliverables|last=|first=|date=|website=autograssmilk.dk|language=en-UK|access-date=2017-03-26}}</ref> There are currently research projects at the [[Dexcel facility]] in [[New Zealand]], [[University of Sydney]]'s FutureDairy site, [[Michigan State University]]'s [[Kellogg Biological Station]] and the [[Swedish University of Agricultural Sciences]]'s research facility [https://www.slu.se/en/faculties/vh/departments/the-swedish-livestock-research-center/ Lövsta Livestock Research Center], where cattle are on pasture and milked by AMS.
* '''Lower milk quality''' –With automatic milking, the number of anaerobic spores, the freezing point increases, the frequency of milk quality failure almost doubles, which fully reflects the quality of milk caused by automatic milking. Although the automatic milking machine cleans the cow's teat and tests the pre-squeezed milk, there is still a phenomenon that the infected milk is not transferred, and the device itself is also lack of cleaning, and the milk is not handled properly. This situation was also confirmed in 2002 when investigating nearly 98 farms in Denmark with automatic milking systems.<ref>{{Cite journal|date=2002-11-01|title=Milk Quality on Danish Farms with Automatic Milking Systems
* '''Possible increase in stress for some cows''' – Cows are social animals, and it has been found that due to dominance of some cows, others will be forced to milk only at night.{{Citation needed|date=September 2010}} Such behaviour is inconsistent with the perception that AM reduces stress by allowing "free choice" of milking time.
* '''Decreased contact between farmer and herd''' – Effective animal husbandry requires that the farmer be fully aware of herd condition. In conventional milking, the cows are observed before milking equipment is attached, and ill or injured cows can be earmarked for attention. Automatic milking decreases the time the farmer has such close contact with the animal, with the possibility that illness may go unnoticed for longer periods and both milk quality and cow welfare suffer. In practice, milk quality sensors at the milking unit attempt to detect changes in milk due to infection, and farmers inspect the herd frequently (Farmers still need to provide bedding for the cows, provide reproductive health services, feed them, and occasionally repair parts of the barn). However this concern has meant that farmers are still tied to a seven-day schedule. Modern automatic milking systems attempt to rectify this problem by gathering data that would not be available in many conventional systems including milk temperature, milk conductivity, milk color including infrared scan, change in milking speed, change in milking time or milk letdown by quarter, cow's weight, cow's activity (movements), time spent ruminating, etc.
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