Academics found that pupils who had taken part in the 10-week programme outperformed another group of children in all of the selected tasks.
Stirling University, which is running the project, now hopes to roll it out to more nurseries as part of a bid to help transform the health of the nation.
Organisers also hope it can help produce elite athletes.
Scotland is currently in the grip of an obesity crisis, with the proportion of adults aged 16 to 64 classed as overweight increasing from 52% to 63% between 1995 and 2010.
Poor diet has been blamed for the upward trend, as well as increasing inactivity fuelled in the young population by the popularity of computer games.
The Scottish Government has already announced that every pupil should get at least two hours a week of physical education in primary school by 2014, with a similar commitment in the early years of secondary.
However, staff from Stirling University's School of Sport believe that, in order for future generations to have the confidence and skills to participate in sport, the basics of physical movement need to be learned between the ages of three and five.
They also believe it is important that physical activity is structured, to teach children skills they can build on in later life.
The department has now developed a 10-week Fundamental Movement Skills qualification, which has been ratified by the Scottish Qualifications Authority.
Under the programme, children are given instruction in a number of basic skills for half an hour each day.
The programme was tested at the privately-run Beaconhurst School's nursery in Bridge of Allan, where child development officers have taken the course.
Stirling student Ross McKechnie evaluated the project's effectiveness by comparing Beaconhurst youngsters with a group of pre-school children.
He and his researchers tested the children on six locomotor skills such as running, jumping and hopping as well as six control skills, including dribbling, throwing and catching a ball.
They filmed the youngsters carrying out the various tasks and, after analysing the data, individual scores were given for each skill based on a standard gross motor development test.
Final results gave an average score for each group on each task and total scores were also recorded.
The results showed that the Beaconhurst group "outperformed the control group in every task" with a particular difference on object control tests.
The study also found significant differences between the two sets of girls, with Beaconhurst girls scoring much higher.
Nicola Duffy, sports participation officer at Stirling University, said: "It is encouraging to see the positive impact the programme is having on the physical literacy and competency of young children.
"Clearly, early intervention is important and, in relation to girls' development, it is fundamental."