They have almost the same meaning, which is "at least". They can be interchangeable depending on the context.
"せめて" is mainly used when you want to mention a minimum requirement in an emotional/subjective way. It indicates your expectations or desires.
"少なくとも" is also used when you want to talk about something in a logical/objective way, and again, in order to mention the minimum requirements for something. It is often used to state something objectively based on factual informaion.
Please sleep at least six hours a day in order to stay healthy.
- [OK]健康でいる為に、毎日せめて6時間は寝てね。
- [OK]健康でいる為に、毎日少なくとも6時間は寝てね。
Please, at least smile for me just one more time. (Because I won't be able to see you for a while.)
- [OK]せめて最後に一度だけあなたの笑顔を見せてね。
- [NG]少なくとも最後に一度だけあなたの笑顔を見せてね。
According to this map, it will take at least 10 minutes from here to the station .
- [NG]この地図によれば、せめてここから駅まで10分はかかる。
- [OK]この地図によれば、少なくともここから駅まで10分はかかる。
If you're interested in learning more information of "せめて", please click HERE