However, the month-on-month figure was better with the €4 rise on May representing a 0.4 percent increase.
The slide in the average property value stemmed primarily from apartment prices with an annualised decline of 2.9 percent and partially due to a change in the typologies subject to mortgage evaluation analysis.
Nevertheless, the average bank evaluation of apartments rose 0.3 percent on May and reached a total of €1,078 per square metre.
In terms of detached residences, the average per square metre price put on 0.8 percent month-on-month, against 0.6 percent in May, to reach €951 up 1.8 percent in annualised terms, against 1.6 percent in May.
Lisbon experienced the sharpest slowdown in the annualised property price rises with June seeing the average rise come in at 5.1 percent, down from the 6.1 percent experienced in May.
The Alentejo region was the only area to see prices firm up in June with the annualised rise hitting 4.5 percent against 1.4 percent in May.