When a laboratory thermometer was dipped inside a hot water beaker, it reads 40°C and when it was taken out, it reads 28°C. What is the temperature of the water in the beaker?

As the temperature reading was 40°C when dipped inside the hot water beaker, the temperature of the water is 40°C. 

As the thermometer is removed the mercury level will drop. That is why it read 28°C outside the beaker.