You can do it if you add Illustrator to the mix.
1) Export from InDesign as PDF
2) Open PDF in Illustrator, export as Photoshop in such color format that allows exporting with layers and preserving text editability, (generally CMYK)
3) Open in Photoshop, convert to RGB, retaining layers, save
4) Import to AE (I guess you already know the required settings and what to do from here)
Kalleheikki Kannisto
Senior Graphic Designer